Compositions and methods of treating cancer using bifidobacterium animalis ssp. lactis

ABSTRACT

Provided herein are methods and compositions related to  Bifidobacterium animalis  ssp. lactis useful as therapeutic agents.

RELATED APPLICATION

This application is a continuation of U.S. patent application Ser. No.16/027,684, filed Jul. 5, 2018, which claims the benefit of priority toU.S. Provisional Patent Application Ser. No. 62/528,669, filed Jul. 5,2017, the entire contents of each of which are expressly incorporatedherein by reference in their entirety.

SEQUENCE LISTING

The instant application contains a Sequence Listing which has beensubmitted electronically in ASCII format and is hereby incorporated byreference in its entirety. Said ASCII copy, created on Jul. 20, 2018, isnamed ETB-007_01_SL.txt and is 2,528,311 bytes in size.

SUMMARY

In certain aspects, provided herein are methods and compositions relatedto the treatment of a cancer in a subject (e.g., a human subject)comprising administering a bacterial composition comprisingBifidobacterium animalis ssp. lactis. In some embodiments, theBifidobacterium animalis ssp. lactis is Bifidobacterium animalis ssp.lactis Strain A (ATCC Deposit Number PTA-125097). In some embodiments,the Bifidobacterium animalis ssp. lactis is a strain comprising at least99% sequence identity (e.g., at least 99.5% sequence identity, at least99.6% sequence identity, at least 99.7% sequence identity, at least99.8% sequence identity, at least 99.9% sequence identity) to thenucleotide sequence of the Bifidobacterium animalis ssp. lactis Strain A(Table 1). In some embodiments, the administration of the bacterialcomposition induces an immune response against a tumor in the subject.In some embodiments, the administration of the bacterial compositioninduces CD3+ immune cell infiltration in the subject. In someembodiments, the administration of the bacterial composition induces MHCClass I upregulation at the tumor site. In some embodiments, theadministration of the bacterial composition treats the cancer in thesubject. In some embodiments, the administration augments a tumormicroenvironment in the subject. In some embodiments, the cancer is acolorectal carcinoma.

In certain embodiments, provided herein are methods of treating asubject who has cancer, comprising administering to the subject abacterial composition comprising Bifidobacterium animalis ssp. lactis(e.g., a killed bacterium, a live bacterium and/or an attenuatedbacterium). In some embodiments, the Bifidobacterium animalis ssp.lactis is Bifidobacterium animalis ssp. lactis Strain A (ATCC DepositNumber PTA-125097). In some embodiments, the Bifidobacterium animalisssp. lactis is a strain comprising at least 99% sequence identity (e.g.,at least 99.5% sequence identity, at least 99.6% sequence identity, atleast 99.7% sequence identity, at least 99.8% sequence identity, atleast 99.9% sequence identity) to the nucleotide sequence of theBifidobacterium animalis ssp. lactis Strain A. In some embodiments, atleast 50%, 60%, 70%, 80%, 85%, 90%, 90%, 91%, 92%, 93%, 94%, 95%, 96%,97%, 98% or 99% of the bacteria in the bacterial composition areBifidobacterium animalis ssp. lactis. In some embodiments, all orsubstantially all of the bacteria in the bacterial formulation areBifidobacterium animalis ssp. lactis. In some embodiments, the bacterialformulation comprises at least 1×10⁵, 5×10⁵, 1×10⁶, 2×10⁶, 3×10⁶, 4×10⁶,5×10⁶, 6×10⁶, 7×10⁶, 8×10⁶, 9×10⁶, 1×10⁷, 2×10⁷, 3×10⁷, 4×10⁷, 5×10⁷,6×10⁷, 7×10⁷, 8×10⁷, 9×10⁷, 1×10⁸, 2×10⁸, 3×10⁸, 4×10⁸, 5×10⁸, 6×10⁸,7×10⁸, 8×10⁸, 9×10⁸ or 1×10⁹ colony forming units of Bifidobacteriumanimalis ssp. lactis.

In certain embodiments, provided herein are bacterial compositionscomprising Bifidobacterium animalis ssp. lactis (e.g., a killedbacterium, a live bacterium and/or an attenuated bacterium). In someembodiments, at least 50%, 60%, 70%, 80%, 85%, 90%, 90%, 91%, 92%, 93%,94%, 95%, 96%, 97%, 98% or 99% of the bacteria in the bacterialcomposition are Bifidobacterium animalis ssp. lactis. In someembodiments, the Bifidobacterium animalis ssp. lactis is Bifidobacteriumanimalis ssp. lactis Strain A (ATCC Deposit Number PTA-125097). In someembodiments, the Bifidobacterium animalis ssp. lactis is a straincomprising at least 99% sequence identity (e.g., at least 99.5% sequenceidentity, at least 99.6% sequence identity, at least 99.7% sequenceidentity, at least 99.8% sequence identity, at least 99.9% sequenceidentity) to the nucleotide sequence of the Bifidobacterium animalisssp. lactis Strain A. In some embodiments, all or substantially all ofthe bacteria in the bacterial formulation are Bifidobacterium animalisssp. lactis. In some embodiments, the bacterial formulation comprises atleast 1×10⁵, 5×10⁵, 1×10⁶, 2×10⁶, 3×10⁶, 4×10⁶, 5×10⁶, 6×10⁶, 7×10⁶,8×10⁶, 9×10⁶, 1×10⁷, 2×10⁷, 3×10⁷, 4×10⁷, 5×10⁷, 6×10⁷, 7×10⁷, 8×10⁷,9×10⁷, 1×10⁸, 2×10⁸, 3×10⁸, 4×10⁸, 5×10⁸, 6×10⁸, 7×10⁸, 8×10⁸, 9×10⁸ or1×10⁹ colony forming units of Bifidobacterium animalis ssp. lactis. Insome embodiments, the bacterial composition comprise at least one strainof Bifidobacterium animalis ssp. lactis having one gene comprising anucleotide base change as identified in Table 6. In some embodiments,the bacterial composition comprise at least one strain ofBifidobacterium animalis ssp. lactis having 1, 2, 3, 4, 5, 6, 7, 8, 9,10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27,28, or 29, genes comprising a nucleotide base change as identified inTable 6. In some embodiments, the bacterial composition comprise atleast one strain of Bifidobacterium animalis ssp. lactis having genescomprising all the nucleotide base change as identified in Table 6.

In some embodiments, provided herein are pharmaceutically activebiomasses (PhABs) derived from and/or comprising Bifidobacteriumanimalis ssp. lactis (e.g., Bifidobacterium animalis ssp. lactis StrainA (ATCC Deposit Number PTA-125097)). In some embodiments, the PhABscomprise whole cells, fractions of cells, supernatant from fermentation,fractions of supernatant and/or extracellular vesicles made fromBifidobacterium animalis ssp. lactis described herein. In someembodiments, the bacterial compositions provided herein compriseBifidobacterium animalis ssp. lactis PhABs provided herein.

In some embodiments, the bacterial composition is administered orally,intravenously, intratumorally, or subcutaneously. In some embodiments,the bacterial composition is administered in 2 or more (e.g., 3 or more,4 or more or 5 or more doses). In some embodiments, the administrationto the subject of the two or more doses are separated by at least 1hour, 2 hours, 3 hours, 4 hours, 5 hours, 6 hours, 7 hours, 8 hours, 9hours, 10 hours, 11 hours, 12 hours, 13 hours, 14 hours, 15 hours, 16hours, 17 hours, 18 hours, 1 day, 2 days, 3 days, 4 days, 5 days, 6days, 7 days, 8 days, 9 days, 10 days, 11 days, 12 days, 13 days, 14days, 15 days, 16 days, 17 days, 18 days, 19 days, 20 days or 21 days.In some embodiments, a second bacterium is administered as part of anecological consortium.

In some embodiments, the method further comprises administering to thesubject an antibiotic. In some embodiments, the method further comprisesadministering to the subject one or more other cancer therapies. In someembodiments, the other cancer therapy is the surgical removal of atumor, the administration of a chemotherapeutic agent, theadministration of radiation therapy, the administration of anantibiotic, the administration of a cancer immunotherapy (e.g., animmune checkpoint inhibitor, a cancer-specific antibody, a cancervaccine, a primed antigen presenting cell, a cancer-specific T cell, acancer-specific chimeric antigen receptor (CAR) T cell, an immuneactivating protein, an adjuvant), and/or the administration of anothertherapeutic bacterium.

In some embodiments, the subject is a mammal. In some embodiments, thesubject is a human. In some embodiments, the subject is a non-humanmammal (e.g., a dog, a cat, a cow, a horse, a pig, a donkey, a goat, acamel, a mouse, a rat, a guinea pig, a sheep, a llama, a monkey, agorilla or a chimpanzee).

In certain embodiments, provided herein is A bioreactor comprisingBifidobacterium animalis ssp. Lactis.

BRIEF DESCRIPTION OF THE FIGURES

FIG. 1 shows inhibition of tumor growth (by volume) by the oraladministration of Bifidobacterium animalis ssp. lactis Strain A in amouse colorectal carcinoma model.

FIG. 2 shows that in a mouse colorectal carcinoma model, the efficacy oforally administered Bifidobacterium animalis ssp. lactis Strain A iscomparable to that of intraperitoneally (i.p.) administered anti-PD-1.

FIG. 3 shows that in a mouse colorectal carcinoma model, the efficacy oforally administered Bifidobacterium animalis ssp. lactis Strain A iscomparable to that of intraperitoneally (i.p.) administered anti-PD-1.

FIG. 4 shows that in a mouse colorectal carcinoma model, the efficacy ofintratumorally Bifidobacterium animalis ssp. lactis Strain A iscomparable to that of intraperitoneally (i.p.) administered anti-PD-1.

FIG. 5 shows that in a mouse melanoma model, treating tumor-inoculatedmice with a combination of Bifidobacterium animalis ssp. lactis Strain Aand anti-PD-L1 inhibits tumor growth in a manner superior to either B.animalis ssp. lactis Strain A or anti-PD-L1 alone.

FIG. 6A shows the tumor volume prior to CD3+ immune cell infiltrate andMHC Class I expression analysis. FIG. 6A shows inhibition of tumorgrowth (by volume) by the oral administration of Bifidobacteriumanimalis ssp. lactis Strain A in a mouse colorectal carcinoma model.

FIG. 6B shows the infiltration of CD3+ immune cells was significantlyincreased in the Bifidobacterium animalis ssp. lactis Strain A grouprelative to the vehicle group.

FIG. 6C shows that Bifidobacterium animalis ssp. lactis Strain A induceda striking upregulation of MHC Class I expression relative to thevehicle group.

FIG. 7 shows an overview of a phase ½ open-label study of the safety,tolerability and efficacy of a Bifidobacterium animalis ssp. lactisStrain A as an oral therapeutic in patients with metastatic colorectalcarcinoma.

FIG. 8 shows that in a mouse colorectal carcinoma model, the efficacy ofa triple combination of Bifidobacterium animalis ssp. lactis Strain A,anti-PD-1, and anti-CTLA4 is greater than that of the combination ofanti-PD-1 and anti-CTLA4.

FIG. 9A and FIG. 9B show a comparison of in vitro signatures of threestrains of Bifidobacterium animalis ssp. lactis (Strain A, Strain B, andStrain C) from a mouse dendritic cell assay. Strain A exhibits an immuneprofile with a decreased induction of pro-tumorigenic cytokines (IL-10,IL-lb, IL-6, IL-8, TNFα) compared to Strain B and Strain C. The cytokinevalues reported represent geometric mean summary of groups (n=3) acrossthe assay.

DETAILED DESCRIPTION General

In certain aspects, provided herein are bacterial compositionscomprising Bifidobacterium animalis ssp. lactis and methods of treatingcancer in a subject comprising administering to the subject a bacterialcomposition comprising Bifidobacterium animalis ssp. lactis.

Definitions

“Adjuvant” or “Adjuvant therapy” broadly refers to an agent that affectsan immunological or physiological response in a patient or subject. Forexample, an adjuvant might increase the presence of an antigen over timeor to an area of interest like a tumor, help absorb an antigenpresenting cell antigen, activate macrophages and lymphocytes andsupport the production of cytokines. By changing an immune response, anadjuvant might permit a smaller dose of an immune interacting agent toincrease the effectiveness or safety of a particular dose of the immuneinteracting agent. For example, an adjuvant might prevent T cellexhaustion and thus increase the effectiveness or safety of a particularimmune interacting agent.

“Administration” broadly refers to a route of administration of acomposition to a subject. Examples of routes of administration includeoral administration, rectal administration, topical administration,inhalation (nasal) or injection. Administration by injection includesintravenous (IV), intramuscular (IM), intratumoral (IT) and subcutaneous(SC) administration. The pharmaceutical compositions described hereincan be administered in any form by any effective route, including butnot limited to intratumoral, oral, parenteral, enteral, intravenous,intraperitoneal, topical, transdermal (e.g., using any standard patch),intradermal, ophthalmic, (intra)nasally, local, non-oral, such asaerosol, inhalation, subcutaneous, intramuscular, buccal, sublingual,(trans)rectal, vaginal, intra-arterial, and intrathecal, transmucosal(e.g., sublingual, lingual, (trans)buccal, (trans)urethral, vaginal(e.g., trans- and perivaginally), intravesical, intrapulmonary,intraduodenal, intragastrical, and intrabronchial. In preferredembodiments, the pharmaceutical compositions described herein areadministered orally, rectally, intratumorally, topically,intravesically, by injection into or adjacent to a draining lymph node,intravenously, by inhalation or aerosol, or subcutaneously.

As used herein, the term “antibody” may refer to both an intact antibodyand an antigen binding fragment thereof. Intact antibodies areglycoproteins that include at least two heavy (H) chains and two light(L) chains inter-connected by disulfide bonds. Each heavy chain includesa heavy chain variable region (abbreviated herein as V_(H)) and a heavychain constant region. Each light chain includes a light chain variableregion (abbreviated herein as V_(L)) and a light chain constant region.The V_(H) and V_(L) regions can be further subdivided into regions ofhypervariability, termed complementarity determining regions (CDR),interspersed with regions that are more conserved, termed frameworkregions (FR). Each V_(H) and V_(L) is composed of three CDRs and fourFRs, arranged from amino-terminus to carboxy-terminus in the followingorder: FR1, CDR1, FR2, CDR2, FR3, CDR3, FR4. The variable regions of theheavy and light chains contain a binding domain that interacts with anantigen. The term “antibody” includes, for example, monoclonalantibodies, polyclonal antibodies, chimeric antibodies, humanizedantibodies, human antibodies, multispecific antibodies (e.g., bispecificantibodies), single-chain antibodies and antigen-binding antibodyfragments.

The terms “antigen binding fragment” and “antigen-binding portion” of anantibody, as used herein, refers to one or more fragments of an antibodythat retain the ability to bind to an antigen. Examples of bindingfragments encompassed within the term “antigen-binding fragment” of anantibody include Fab, Fab′, F(ab′)₂, Fv, scFv, disulfide linked Fv, Fd,diabodies, single-chain antibodies, NANOBODIES®, isolated CDRH3, andother antibody fragments that retain at least a portion of the variableregion of an intact antibody. These antibody fragments can be obtainedusing conventional recombinant and/or enzymatic techniques and can bescreened for antigen binding in the same manner as intact antibodies.

“Cancer” broadly refers to an uncontrolled, abnormal growth of a host'sown cells leading to invasion of surrounding tissue and potentiallytissue distal to the initial site of abnormal cell growth in the host.Major classes include carcinomas which are cancers of the epithelialtissue (e.g., skin, squamous cells); sarcomas which are cancers of theconnective tissue (e.g., bone, cartilage, fat, muscle, blood vessels,etc.); leukemias which are cancers of blood forming tissue (e.g., bonemarrow tissue); lymphomas and myelomas which are cancers of immunecells; and central nervous system cancers which include cancers frombrain and spinal tissue. “Cancer(s),” “neoplasm(s),” and “tumor(s)” areused herein interchangeably. As used herein, “cancer” refers to alltypes of cancer or neoplasm or malignant tumors including leukemias,carcinomas and sarcomas, whether new or recurring. Specific examples ofcancers are: carcinomas, sarcomas, myelomas, leukemias, lymphomas andmixed type tumors. Non-limiting examples of cancers are new or recurringcancers of the brain, melanoma, bladder, breast, cervix, colon, head andneck, kidney, lung, non-small cell lung, mesothelioma, ovary, prostate,sarcoma, stomach, uterus and medulloblastoma. Pediatric and adult tumorsinclude, but not limited to, those of bladder, brain, breast, bone,cervix, colon, connective tissue, fat, head and neck, kidney, liver,lung, mesothelium, melanocytes (melanoma), muscle, ovary, pancreas,prostate, stomach, small intestine, and uterus

The term “decrease” or “deplete” means a change, such that thedifference is, depending on circumstances, at least 10%, 20%, 30%, 40%,50%, 60%, 70%, 80%, 90%, 1/100, 1/1000, 1/10,000, 1/100,000, 1/1,000,000or undetectable after treatment when compared to a pre-treatment state.

The term “ecological consortium” is a group of bacteria which tradesmetabolites and positively co-regulates one another, in contrast to twobacteria which induce host synergy through activating complementary hostpathways for improved efficacy.

The term “epitope” means a protein determinant capable of specificbinding to an antibody. Epitopes usually consist of chemically activesurface groupings of molecules such as amino acids or sugar side chains.Certain epitopes can be defined by a particular sequence of amino acidsto which an antibody is capable of binding.

The term “gene” is used broadly to refer to any nucleic acid associatedwith a biological function. The term “gene” applies to a specificgenomic sequence, as well as to a cDNA or an mRNA encoded by thatgenomic sequence.

“Identity” as between nucleic acid sequences of two nucleic acidmolecules can be determined as a percentage of identity using knowncomputer algorithms such as the “FASTA” program, using for example, thedefault parameters as in Pearson et al. (1988) Proc. Natl. Acad. Sci.USA 85:2444 (other programs include the GCG program package (Devereux,J., et al., Nucleic Acids Research 12(I):387 (1984)), BLASTP, BLASTN,FASTA Atschul, S. F., et al., J Molec Biol 215:403 (1990); Guide to HugeComputers, Mrtin J. Bishop, ed., Academic Press, San Diego, 1994, andCarillo et al. (1988) SIAM J Applied Math 48:1073). For example, theBLAST function of the National Center for Biotechnology Informationdatabase can be used to determine identity. Other commercially orpublicly available programs include, DNAStar “MegAlign” program(Madison, Wis.) and the University of Wisconsin Genetics Computer Group(UWG) “Gap” program (Madison Wis.)).

“Immunotherapy” is treatment that uses a subject's immune system totreat cancer and includes, for example, checkpoint inhibitors, cancervaccines, cytokines, cell therapy, CAR-T cells, and dendritic celltherapy.

The term “increase” means a change, such that the difference is,depending on circumstances, at least 10%, 20%, 30%, 40%, 50%, 60%, 70%,80%, 90%, 2-fold, 4-fold, 10-fold, 100-fold, 10{circumflex over ( )}3fold, 10{circumflex over ( )}4 fold, 10{circumflex over ( )}5 fold,10{circumflex over ( )}6 fold, and/or 10{circumflex over ( )}7 foldgreater after treatment when compared to a pre-treatment state.Properties that may be increased include immune cells, bacterial cells,stromal cells, myeloid derived suppressor cells, fibroblasts,metabolites, and cytokines.

“Innate immune agonists” or “immuno-adjuvants” are small molecules,proteins, or other agents that specifically target innate immunereceptors including Toll-Like Receptors, NOD receptors, STING Pathwaycomponents. For example, LPS is a TLR-4 agonist that is bacteriallyderived or synthesized and aluminum can be used as an immune stimulatingadjuvant. immuno-adjuvants are a specific class of broader adjuvant oradjuvant therapy.

The term “isolated” or “enriched” encompasses a microbe, bacteria orother entity or substance that has been (1) separated from at least someof the components with which it was associated when initially produced(whether in nature or in an experimental setting), and/or (2) produced,prepared, purified, and/or manufactured by the hand of man. Isolatedmicrobes may be separated from at least about 10%, about 20%, about 30%,about 40%, about 50%, about 60%, about 70%, about 80%, about 90%, ormore of the other components with which they were initially associated.In some embodiments, isolated microbes are more than about 80%, about85%, about 90%, about 91%, about 92%, about 93%, about 94%, about 95%,about 96%, about 97%, about 98%, about 99%, or more than about 99% pure.As used herein, a substance is “pure” if it is substantially free ofother components. The terms “purify,” “purifying” and “purified” referto a microbe or other material that has been separated from at leastsome of the components with which it was associated either wheninitially produced or generated (e.g., whether in nature or in anexperimental setting), or during any time after its initial production.A microbe or a microbial population may be considered purified if it isisolated at or after production, such as from a material or environmentcontaining the microbe or microbial population, and a purified microbeor microbial population may contain other materials up to about 10%,about 20%, about 30%, about 40%, about 50%, about 60%, about 70%, about80%, about 90%, or above about 90% and still be considered “isolated.”In some embodiments, purified microbes or microbial population are morethan about 80%, about 85%, about 90%, about 91%, about 92%, about 93%,about 94%, about 95%, about 96%, about 97%, about 98%, about 99%, ormore than about 99% pure. In the instance of microbial compositionsprovided herein, the one or more microbial types present in thecomposition can be independently purified from one or more othermicrobes produced and/or present in the material or environmentcontaining the microbial type. Microbial compositions and the microbialcomponents thereof are generally purified from residual habitatproducts.

As used herein, a gene is “overexpressed” in a bacteria if it isexpressed at a higher level in an engineered bacteria under at leastsome conditions than it is expressed by a wild-type bacteria of the samespecies under the same conditions. Similarly, a gene is “underexpressed”in a bacteria if it is expressed at a lower level in an engineeredbacteria under at least some conditions than it is expressed by awild-type bacteria of the same species under the same conditions.

The terms “polynucleotide” and “nucleic acid” are used interchangeably.They refer to a polymeric form of nucleotides of any length, eitherdeoxyribonucleotides or ribonucleotides, or analogs thereof.Polynucleotides may have any three-dimensional structure, and mayperform any function. The following are non-limiting examples ofpolynucleotides: coding or non-coding regions of a gene or genefragment, loci (locus) defined from linkage analysis, exons, introns,messenger RNA (mRNA), transfer RNA, ribosomal RNA, ribozymes, cDNA,recombinant polynucleotides, branched polynucleotides, plasmids,vectors, isolated DNA of any sequence, isolated RNA of any sequence,nucleic acid probes, and primers. A polynucleotide may comprise modifiednucleotides, such as methylated nucleotides and nucleotide analogs. Ifpresent, modifications to the nucleotide structure may be impartedbefore or after assembly of the polymer. A polynucleotide may be furthermodified, such as by conjugation with a labeling component. In allnucleic acid sequences provided herein, U nucleotides areinterchangeable with T nucleotides.

“Operational taxonomic units” and “OTU(s)” refer to a terminal leaf in aphylogenetic tree and is defined by a nucleic acid sequence, e.g., theentire genome, or a specific genetic sequence, and all sequences thatshare sequence identity to this nucleic acid sequence at the level ofspecies. In some embodiments the specific genetic sequence may be the16S sequence or a portion of the 16S sequence. In other embodiments, theentire genomes of two entities are sequenced and compared. In anotherembodiment, select regions such as multilocus sequence tags (MLST),specific genes, or sets of genes may be genetically compared. For 16S,OTUs that share ≥97% average nucleotide identity across the entire 16Sor some variable region of the 16S are considered the same OTU. See e.g.Claesson M J, Wang Q, O'Sullivan O, Greene-Diniz R, Cole J R, Ross R P,and O'Toole P W. 2010. Comparison of two next-generation sequencingtechnologies for resolving highly complex microbiota composition usingtandem variable 16S rRNA gene regions. Nucleic Acids Res 38: e200.Konstantinidis K T, Ramette A, and Tiedje J M. 2006. The bacterialspecies definition in the genomic era. Philos Trans R Soc Lond B BiolSci 361: 1929-1940. For complete genomes, MLSTs, specific genes, otherthan 16S, or sets of genes OTUs that share ≥95% average nucleotideidentity are considered the same OTU. See e.g., Achtman M, and Wagner M.2008. Microbial diversity and the genetic nature of microbial species.Nat. Rev. Microbiol. 6: 431-440. Konstantinidis K T, Ramette A, andTiedje J M. 2006. The bacterial species definition in the genomic era.Philos Trans R Soc Lond B Biol Sci 361: 1929-1940. OTUs are frequentlydefined by comparing sequences between organisms. Generally, sequenceswith less than 95% sequence identity are not considered to form part ofthe same OTU. OTUs may also be characterized by any combination ofnucleotide markers or genes, in particular highly conserved genes (e.g.,“house-keeping” genes), or a combination thereof. Operational TaxonomicUnits (OTUs) with taxonomic assignments made to, e.g., genus, species,and phylogenetic clade are provided herein.

As used herein, “specific binding” refers to the ability of an antibodyto bind to a predetermined antigen or the ability of a polypeptide tobind to its predetermined binding partner. Typically, an antibody orpolypeptide specifically binds to its predetermined antigen or bindingpartner with an affinity corresponding to a K_(D) of about 10⁻⁷ M orless, and binds to the predetermined antigen/binding partner with anaffinity (as expressed by K_(D)) that is at least 10 fold less, at least100 fold less or at least 1000 fold less than its affinity for bindingto a non-specific and unrelated antigen/binding partner (e.g., BSA,casein). Alternatively, specific binding applies more broadly to a twocomponent system where one component is a protein, lipid, orcarbohydrate or combination thereof and engages with the secondcomponent which is a protein, lipid, carbohydrate or combination thereofin a specific way.

The terms “subject” or “patient” refers to any animal. A subject or apatient described as “in need thereof” refers to one in need of atreatment for a disease. Mammals (i.e., mammalian animals) includehumans, laboratory animals (e.g., primates, rats, mice), livestock(e.g., cows, sheep, goats, pigs), and household pets (e.g., dogs, cats,rodents). For example, the subject may be a non-human mammal includingbut not limted to of a dog, a cat, a cow, a horse, a pig, a donkey, agoat, a camel, a mouse, a rat, a guinea pig, a sheep, a llama, a monkey,a gorilla or a chimpanzee. The subject or patient may be healthy, or maybe suffering from a neoplasm at any developmental stage, wherein any ofthe stages are either caused by or opportunistically supported of acancer associated or causative pathogen, or may be at risk of developinga neoplasm, or transmitting to others a cancer associated or cancercausative pathogen. In some embodiments patients have lung cancer,bladder cancer, prostate cancer, ovarian cancer, and/or melanoma. Thepatients may have tumors that show enhanced macropinocytosis with theunderlying genomics of this process including Ras activation. In otherembodiments patients suffer from other cancers. In some embodiments, thesubject has undergone a cancer therapy.

“Strain” refers to a member of a bacterial species with a geneticsignature such that it may be differentiated from closely-relatedmembers of the same bacterial species. The genetic signature may be theabsence of all or part of at least one gene, the absence of all or partof at least on regulatory region (e.g., a promoter, a terminator, ariboswitch, a ribosome binding site), the absence (“curing”) of at leastone native plasmid, the presence of at least one recombinant gene, thepresence of at least one mutated gene, the presence of at least oneforeign gene (a gene derived from another species), the presence atleast one mutated regulatory region (e.g., a promoter, a terminator, ariboswitch, a ribosome binding site), the presence of at least onenon-native plasmid, the presence of at least one antibiotic resistancecassette, or a combination thereof. Genetic signatures between differentstrains may be identified by PCR amplification optionally followed byDNA sequencing of the genomic region(s) of interest or of the wholegenome. In the case in which one strain (compared with another of thesame species) has gained or lost antibiotic resistance or gained or losta biosynthetic capability (such as an auxotrophic strain), strains maybe differentiated by selection or counter-selection using an antibioticor nutrient/metabolite, respectively.

As used herein, the term “treating” a disease in a subject or “treating”a subject having or suspected of having a disease refers to subjectingthe subject to a pharmaceutical treatment, e.g., the administration ofone or more agents, such that at least one symptom of the disease isdecreased or prevented from worsening. Thus, in one embodiment,“treating” refers inter alia to delaying progression, expeditingremission, inducing remission, augmenting remission, speeding recovery,increasing efficacy of or decreasing resistance to alternativetherapeutics, or a combination thereof. In certain embodiments, a canceris treated if the subject experiences a reduction in tumor size, areduced number of tumors, a reduction in tumor growth, a reduction incancer metastisis and/or a reduced number of total cancer cellsfollowing treatment than would be expected in the absence of treatment.

Bacteria

In certain aspects, provided herein are bacterial compositionscomprising Bifidobacterium animalis ssp. lactis (e.g.,. an effectiveamount of Bifidobacterium animalis ssp. lactis) and methods of using abacterial composition comprising Bifidobacterium animalis ssp. lactis.In some embodiments, the Bifidobacterium animalis ssp. lactis isBifidobacterium animalis ssp. lactis Strain A (ATCC Deposit NumberPTA-125097). In some embodiments, the bacterial composition comprise aPhAB made from or comprising a Bifidobacterium animalis ssp. lactisdescribed herein. In some embodiments, the Bifidobacterium animalis ssp.lactis is a strain comprising at least 99% sequence identity (e.g., atleast 99.5% sequence identity, at least 99.6% sequence identity, atleast 99.7% sequence identity, at least 99.8% sequence identity, atleast 99.9% sequence identity) to the nucleotide sequence of theBifidobacterium animalis ssp. lactis Strain A.

Under the terms of the Budapest Treaty on the International Recognitionof the Deposit of Microorganisms for the Purpose of Patent Procedure,the Bifidobacterium animalis ssp. Lactis Strain A was deposited on Apr.27, 2018, with the American Type Culture Collection (ATCC) of 10801University Boulevard, Manassas, Va. 20110-2209 USA and was assigned ATCCAccession Number PTA-125097.

Applicant represents that the ATCC is a depository affording permanenceof the deposit and ready accessibility thereto by the public if a patentis granted. All restrictions on the availability to the public of thematerial so deposited will be irrevocably removed upon the granting of apatent. The material will be available during the pendency of the patentapplication to one determined by the Commissioner to be entitled theretounder 37 CFR 1.14 and 35 U.S.C. 122. The deposited material will bemaintained with all the care necessary to keep it viable anduncontaminated for a period of at least five years after the most recentrequest for the furnishing of a sample of the deposited plasmid, and inany case, for a period of at least thirty (30) years after the date ofdeposit or for the enforceable life of the patent, whichever period islonger. Applicant acknowledges its duty to replace the deposit shouldthe depository be unable to furnish a sample when requested due to thecondition of the deposit.

In some embodiments, the bacteria described herein are modified toimprove colonization and/or engraftment in the mammaliangastrointestinal tract (e.g., modified metabolism, such as improvedmucin degradation, enhanced competition profile, increased motility,increased adhesion to gut epithelial cells, modified chemotaxis). Insome embodiments, the bacteria described herein are modified to enhancetheir immunomodulatory and/or therapeutic effect (e.g., either alone orin combination with another therapeutic agent). In some embodiments, thebacteria described herein are modified to enhance immune activation(e.g., through modified production of polysaccharides, pili, fimbriae,adhesins, outer membrane vesicles). In some embodiments, the bacteriadescribed herein are modified to improve bacterial manufacturing (e.g.,higher oxygen tolerance, improved freeze-thaw tolerance, shortergeneration times).

In certain embodiments, the Bifidobacterium animalis ssp. lactis isgrown in Reinforced Clostridium medium (RCM medium) (ATCC 2107 or mediumfrom other manufacturer), Lactobacilli MRS medium (LMRS medium), and/orBifido agar. Alternatively, Bifidobactrium animalis ssp. lactis is grownusing RCM medium ATCC 1053 and/or Trypticase soy agar/broth withdefibrimated sheep blood ATCC 260 per the manufacturer's instructions.

The nucleotide sequence of the Bifidobacterium animalis ssp. lactisStrain A is shown in Table 1.

Lengthy table referenced here US20210093680A1-20210401-T00001 Pleaserefer to the end of the specification for access instructions.

Bacterial Compositions

In certain aspects, provided herein are bacterial compositionscomprising Bifidobacterium animalis ssp. Lactis. In some embodiments,the Bifidobacterium animalis ssp. lactis is Bifidobacterium animalisssp. lactis Strain A (ATCC Deposit Number PTA-125097). In someembodiments, the bacterial composition comprise a PhAB made from orcomprising a Bifidobacterium animalis ssp. lactis described herein. Insome embodiments, the Bifidobacterium animalis ssp. lactis is a straincomprising at least 99% sequence identity (e.g., at least 99.5% sequenceidentity, at least 99.6% sequence identity, at least 99.7% sequenceidentity, at least 99.8% sequence identity, at least 99.9% sequenceidentity) to the nucleotide sequence of the Bifidobacterium animalisssp. lactis Strain A. In some embodiments, the bacterial formulationcomprises a bacterium and/or a combination of bacteria described hereinand a pharmaceutically acceptable carrier.

In certain embodiments, at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%,90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% of the bacteria inthe bacterial composition are Bifidobacterium animalis ssp. lactis. Incertain embodiments, substantially all of the bacteria in the bacterialcomposition are Bifidobacterium animalis ssp. lactis. In certainembodiments, the bacterial composition comprises at least 1×10³ colonyforming units (CFUs), 1×10⁴ colony forming units (CFUs), 1×10⁵ colonyforming units (CFUs), 5×10⁵ colony forming units (CFUs), 1×10⁶ colonyforming units (CFUs), 2×10⁶ colony forming units (CFUs), 3×10⁶ colonyforming units (CFUs), 4×10⁶ colony forming units (CFUs), 5×10⁶ colonyforming units (CFUs), 6×10⁶ colony forming units (CFUs), 7×10⁶ colonyforming units (CFUs), 8×10⁶ colony forming units (CFUs), 9×10⁶ colonyforming units (CFUs), 1×10⁷ colony forming units (CFUs), 2×10⁷ colonyforming units (CFUs), 3×10⁷ colony forming units (CFUs), 4×10⁷ colonyforming units (CFUs), 5×10⁷ colony forming units (CFUs), 6×10⁷ colonyforming units (CFUs), 7×10⁷ colony forming units (CFUs), 8×10⁷ colonyforming units (CFUs), 9×10⁷ colony forming units (CFUs), 1×10⁸ colonyforming units (CFUs), 2×10⁸ colony forming units (CFUs), 3×10⁸ colonyforming units (CFUs), 4×10⁸ colony forming units (CFUs), 5×10⁸ colonyforming units (CFUs), 6×10⁸ colony forming units (CFUs), 7×10⁸ colonyforming units (CFUs), 8×10⁸ colony forming units (CFUs), 9×10⁸ colonyforming units (CFUs), 1×10⁹ colony forming units (CFUs), 5×10⁹ colonyforming units (CFUs), 1×10¹⁰ colony forming units (CFUs) 5×10¹⁰ colonyforming units (CFUs), 1×10¹¹ colony forming units (CFUs) 5×10¹¹ colonyforming units (CFUs), 1×10¹² colony forming units (CFUs) 5×10¹² colonyforming units (CFUs), 1×10¹³ colony forming units (CFUs) ofBifidobacterium animalis ssp. lactis.

In some embodiments, Probiotic formulations containing Bifidobacteriumanimalis ssp. lactis are provided as encapsulated, enteric coated, orpowder forms, with doses ranging up to 10¹¹ cfu (e.g., upto 10¹⁰ cfu).In some embodiments, the composition comprises 5×10¹¹ cfu ofBifidobacterium animalis ssp. lactis and 10% (w/w) corn starch in acapsule. The capsule is enteric coated for duodenal release at pH5.5 Insome embodiments, the capsule is enteric coated for duodenal release atpH 5.5. In some embodiments, the composition comprises a powder offreeze-dried Bifidobacterium animalis ssp. lactis which is deemed“Qualified Presumption of Safety” (QPS) status. In some embodiments, thecomposition is stable at frozen or refrigerated temperature.

Methods for producing microbial compositions may include three mainprocessing steps. The steps are: organism banking, organism production,and preservation. In certain embodiments, a sample that contains anabundance of Bifidobacterium animalis ssp. lactis may be cultured byavoiding an isolation step.

For banking, the strains included in the microbial composition may be(1) isolated directly from a specimen or taken from a banked stock, (2)optionally cultured on a nutrient agar or broth that supports growth togenerate viable biomass, and (3) the biomass optionally preserved inmultiple aliquots in long-term storage.

In embodiments using a culturing step, the agar or broth may containnutrients that provide essential elements and specific factors thatenable growth. An example would be a medium composed of 20 g/L glucose,10 g/L yeast extract, 10 g/L soy peptone, 2 g/L citric acid, 1.5 g/Lsodium phosphate monobasic, 100 mg/L ferric ammonium citrate, 80 mg/Lmagnesium sulfate, 10 mg/L hemin chloride, 2 mg/L calcium chloride, 1mg/L menadione. Another example would be a medium composed of 10 g/Lbeef extract, 10 g/L peptone, 5 g/L sodium chloride, 5 g/L dextrose, 3g/L yeast extract, 3 g/L sodium acetate, 1 g/L soluble starch, and 0.5g/L L-cysteine HCl, at pH 6.8. A variety of microbiological media andvariations are well known in the art (e.g., R. M. Atlas, Handbook ofMicrobiological Media (2010) CRC Press). Culture media can be added tothe culture at the start, may be added during the culture, or may beintermittently/continuously flowed through the culture. The strains inthe bacterial composition may be cultivated alone, as a subset of themicrobial composition, or as an entire collection comprising themicrobial composition. As an example, a first strain may be cultivatedtogether with a second strain in a mixed continuous culture, at adilution rate lower than the maximum growth rate of either cell toprevent the culture from washing out of the cultivation.

The inoculated culture is incubated under favorable conditions for atime sufficient to build biomass. For microbial compositions for humanuse this is often at 37° C. temperature, pH, and other parameter withvalues similar to the normal human niche. The environment may beactively controlled, passively controlled (e.g., via buffers), orallowed to drift. For example, for anaerobic bacterial compositions, ananoxic/reducing environment may be employed. This can be accomplished byaddition of reducing agents such as cysteine to the broth, and/orstripping it of oxygen. As an example, a culture of a bacterialcomposition may be grown at 37° C., pH 7, in the medium above,pre-reduced with 1 g/L cysteine-HCl.

When the culture has generated sufficient biomass, it may be preservedfor banking. The organisms may be placed into a chemical milieu thatprotects from freezing (adding ‘cryoprotectants’), drying(‘lyoprotectants’), and/or osmotic shock (‘osmoprotectants’), dispensinginto multiple (optionally identical) containers to create a uniformbank, and then treating the culture for preservation. Containers aregenerally impermeable and have closures that assure isolation from theenvironment. Cryopreservation treatment is accomplished by freezing aliquid at ultra-low temperatures (e.g., at or below −80° C.). Driedpreservation removes water from the culture by evaporation (in the caseof spray drying or ‘cool drying’) or by sublimation (e.g., for freezedrying, spray freeze drying). Removal of water improves long-termmicrobial composition storage stability at temperatures elevated abovecryogenic conditions. If the microbial composition comprises, forexample, spore forming species and results in the production of spores,the final composition may be purified by additional means such asdensity gradient centrifugation and preserved using the techniques[?]described above[?]. Microbial composition banking may be done byculturing and preserving the strains individually, or by mixing thestrains together to create a combined bank. As an example ofcryopreservation, a microbial composition culture may be harvested bycentrifugation to pellet the cells from the culture medium, thesupernatant decanted and replaced with fresh culture broth containing15% glycerol. The culture can then be aliquoted into 1 mL cryotubes,sealed, and placed at −80° C. for long-term viability retention. Thisprocedure achieves acceptable viability upon recovery from frozenstorage.

Microbial production may be conducted using similar culture steps tobanking, including medium composition and culture conditions describedabove. It may be conducted at larger scales of operation, especially forclinical development or commercial production. At larger scales, theremay be several subcultivations of the microbial composition prior to thefinal cultivation. At the end of cultivation, the culture is harvestedto enable further formulation into a dosage form for administration.This can involve concentration, removal of undesirable mediumcomponents, and/or introduction into a chemical milieu that preservesthe microbial composition and renders it acceptable for administrationvia the chosen route. For example, a microbial composition may becultivated to a concentration of 10¹⁰ CFU/mL, then concentrated 20-foldby tangential flow microfiltration; the spent medium may be exchanged bydiafiltering with a preservative medium consisting of 2% gelatin, 100 mMtrehalose, and 10 mM sodium phosphate buffer. The suspension can then befreeze-dried to a powder and titrated.

After drying, the powder may be blended to an appropriate potency, andmixed with other cultures and/or a filler such as microcrystallinecellulose for consistency and ease of handling, and the bacterialcomposition formulated as provided herein.

In certain aspects, provided are bacterial compositions foradministration subjects. In some embodiments, the bacterial compositionsare combined with additional active and/or inactive materials in orderto produce a final product, which may be in single dosage unit or in amulti-dose format.

In some embodiments, the composition comprises at least onecarbohydrate. A “carbohydrate” refers to a sugar or polymer of sugars.The terms “saccharide,” “polysaccharide,” “carbohydrate,” and“oligosaccharide” may be used interchangeably. Most carbohydrates arealdehydes or ketones with many hydroxyl groups, usually one on eachcarbon atom of the molecule. Carbohydrates generally have the molecularformula C_(n)H_(2n)O_(n). A carbohydrate may be a monosaccharide, adisaccharide, trisaccharide, oligosaccharide, or polysaccharide. Themost basic carbohydrate is a monosaccharide, such as glucose, sucrose,galactose, mannose, ribose, arabinose, xylose, and fructose.Disaccharides are two joined monosaccharides. Exemplary disaccharidesinclude sucrose, maltose, cellobiose, and lactose. Typically, anoligosaccharide includes between three and six monosaccharide units(e.g., raffinose, stachyose), and polysaccharides include six or moremonosaccharide units. Exemplary polysaccharides include starch,glycogen, and cellulose. Carbohydrates may contain modified saccharideunits such as 2′-deoxyribose wherein a hydroxyl group is removed,2′-fluororibose wherein a hydroxyl group is replaced with a fluorine, orN-acetylglucosamine, a nitrogen-containing form of glucose (e.g.,2′-fluororibose, deoxyribose, and hexose). Carbohydrates may exist inmany different forms, for example, conformers, cyclic forms, acyclicforms, stereoisomers, tautomers, anomers, and isomers.

In some embodiments, the composition comprises at least one lipid. Asused herein, a “lipid” includes fats, oils, triglycerides, cholesterol,phospholipids, fatty acids in any form including free fatty acids. Fats,oils and fatty acids can be saturated, unsaturated (cis or trans) orpartially unsaturated (cis or trans). In some embodiments the lipidcomprises at least one fatty acid selected from lauric acid (12:0),myristic acid (14:0), palmitic acid (16:0), palmitoleic acid (16:1),margaric acid (17:0), heptadecenoic acid (17:1), stearic acid (18:0),oleic acid (18:1), linoleic acid (18:2), linolenic acid (18:3),octadecatetraenoic acid (18:4), arachidic acid (20:0), eicosenoic acid(20:1), eicosadienoic acid (20:2), eicosatetraenoic acid (20:4),eicosapentaenoic acid (20:5) (EPA), docosanoic acid (22:0), docosenoicacid (22:1), docosapentaenoic acid (22:5), docosahexaenoic acid (22:6)(DHA), and tetracosanoic acid (24:0). In some embodiments thecomposition comprises at least one modified lipid, for example a lipidthat has been modified by cooking.

In some embodiments, the composition comprises at least one supplementalmineral or mineral source. Examples of minerals include, withoutlimitation: chloride, sodium, calcium, iron, chromium, copper, iodine,zinc, magnesium, manganese, molybdenum, phosphorus, potassium, andselenium. Suitable forms of any of the foregoing minerals includesoluble mineral salts, slightly soluble mineral salts, insoluble mineralsalts, chelated minerals, mineral complexes, non-reactive minerals suchas carbonyl minerals, and reduced minerals, and combinations thereof.

In some embodiments, the composition comprises at least one supplementalvitamin. The at least one vitamin can be fat-soluble or water solublevitamins. Suitable vitamins include but are not limited to vitamin C,vitamin A, vitamin E, vitamin B12, vitamin K, riboflavin, niacin,vitamin D, vitamin B6, folic acid, pyridoxine, thiamine, pantothenicacid, and biotin. Suitable forms of any of the foregoing are salts ofthe vitamin, derivatives of the vitamin, compounds having the same orsimilar activity of the vitamin, and metabolites of the vitamin.

In some embodiments, the composition comprises an excipient.Non-limiting examples of suitable excipients include a buffering agent,a preservative, a stabilizer, a binder, a compaction agent, a lubricant,a dispersion enhancer, a disintegration agent, a flavoring agent, asweetener, and a coloring agent.

In some embodiments, the excipient is a buffering agent. Non-limitingexamples of suitable buffering agents include sodium citrate, magnesiumcarbonate, magnesium bicarbonate, calcium carbonate, and calciumbicarbonate.

In some embodiments, the excipient comprises a preservative.Non-limiting examples of suitable preservatives include antioxidants,such as alpha-tocopherol and ascorbate, and antimicrobials, such asparabens, chlorobutanol, and phenol.

In some embodiments, the composition comprises a binder as an excipient.Non-limiting examples of suitable binders include starches,pregelatinized starches, gelatin, polyvinylpyrolidone, cellulose,methylcellulose, sodium carboxymethylcellulose, ethylcellulose,polyacrylamides, polyvinyloxoazolidone, polyvinylalcohols, C₁₂-C₁₈ fattyacid alcohol, polyethylene glycol, polyols, saccharides,oligosaccharides, and combinations thereof.

In some embodiments, the composition comprises a lubricant as anexcipient. Non-limiting examples of suitable lubricants includemagnesium stearate, calcium stearate, zinc stearate, hydrogenatedvegetable oils, sterotex, polyoxyethylene monostearate, talc,polyethyleneglycol, sodium benzoate, sodium lauryl sulfate, magnesiumlauryl sulfate, and light mineral oil.

In some embodiments, the composition comprises a dispersion enhancer asan excipient. Non-limiting examples of suitable dispersants includestarch, alginic acid, polyvinylpyrrolidones, guar gum, kaolin,bentonite, purified wood cellulose, sodium starch glycolate,isoamorphous silicate, and microcrystalline cellulose as high HLBemulsifier surfactants.

In some embodiments, the composition comprises a disintegrant as anexcipient. In some embodiments the disintegrant is a non-effervescentdisintegrant. Non-limiting examples of suitable non-effervescentdisintegrants include starches such as corn starch, potato starch,pregelatinized and modified starches thereof, sweeteners, clays, such asbentonite, micro-crystalline cellulose, alginates, sodium starchglycolate, gums such as agar, guar, locust bean, karaya, pectin, andtragacanth. In some embodiments the disintegrant is an effervescentdisintegrant. Non-limiting examples of suitable effervescentdisintegrants include sodium bicarbonate in combination with citricacid, and sodium bicarbonate in combination with tartaric acid.

In some embodiments, the bacterial formulation comprises an entericcoating or micro encapsulation. In certain embodiments, the entericcoating or micro encapsulation improves targeting to a desired region ofthe gastrointestinal tract. For example, in certain embodiments, thebacterial composition comprises an enteric coating and/or microcapsulesthat dissolves at a pH associated with a particular region of thegastrointestinal tract. In some embodiments, the enteric coating and/ormicrocapsules dissolve at a pH of about 5.5-6.2 to release in theduodenum, at a pH value of about 7.2-7.5 to release in the ileum, and/orat a pH value of about 5.6-6.2 to release in the colon. Exemplaryenteric coatings and microcapsules are described, for example, in U.S.Pat. Pub. No. 2016/0022592, which is hereby incorporated by reference inits entirety.

In some embodiments, the composition is a food product (e.g., a food orbeverage) such as a health food or beverage, a food or beverage forinfants, a food or beverage for pregnant women, athletes, seniorcitizens or other specified group, a functional food, a beverage, a foodor beverage for specified health use, a dietary supplement, a food orbeverage for patients, or an animal feed. Specific examples of the foodsand beverages include various beverages such as juices, refreshingbeverages, tea beverages, drink preparations, jelly beverages, andfunctional beverages; alcoholic beverages such as beers;carbohydrate-containing foods such as rice food products, noodles,breads, and pastas; paste products such as fish hams, sausages, pasteproducts of seafood; retort pouch products such as curries, food dressedwith a thick starchy sauces, and Chinese soups; soups; dairy productssuch as milk, dairy beverages, ice creams, cheeses, and yogurts;fermented products such as fermented soybean pastes, yogurts, fermentedbeverages, and pickles; bean products; various confectionery products,including biscuits, cookies, and the like, candies, chewing gums,gummies, cold desserts including jellies, cream caramels, and frozendesserts; instant foods such as instant soups and instant soy-beansoups; microwavable foods; and the like. Further, the examples alsoinclude health foods and beverages prepared in the forms of powders,granules, tablets, capsules, liquids, pastes, and jellies.

In certain embodiments, the bacteria disclosed herein are administeredin conjunction with a prebiotic to the subject. Prebiotics arecarbohydrates which are generally indigestible by a host animal and areselectively fermented or metabolized by bacteria. Prebiotics may beshort-chain carbohydrates (e.g., oligosaccharides) and/or simple sugars(e.g., mono- and di-saccharides) and/or mucins (heavily glycosylatedproteins) that alter the composition or metabolism of a microbiome inthe host. The short chain carbohydrates are also referred to asoligosaccharides, and usually contain from 2 or 3 and up to 8, 9, 10, 15or more sugar moieties. When prebiotics are introduced to a host, theprebiotics affect the bacteria within the host and do not directlyaffect the host. In certain aspects, a prebiotic composition canselectively stimulate the growth and/or activity of one of a limitednumber of bacteria in a host. Prebiotics include oligosaccharides suchas fructooligosaccharides (FOS) (including inulin),galactooligosaccharides (GOS), trans-galactooligosaccharides,xylooligosaccharides (XOS), chitooligosaccharides (COS), soyoligosaccharides (e.g., stachyose and raffinose) gentiooligosaccharides,isomaltooligosaccharides, mannooligosaccharides, maltooligosaccharidesand mannanoligosaccharides. Oligosaccharides are not necessarily singlecomponents, and can be mixtures containing oligosaccharides withdifferent degrees of oligomerization, sometimes including the parentdisaccharide and the monomeric sugars. Various types of oligosaccharidesare found as natural components in many common foods, including fruits,vegetables, milk, and honey. Specific examples of oligosaccharides arelactulose, lactosucrose, palatinose, glycosyl sucrose, guar gum, gumArabic, tagalose, amylose, amylopectin, pectin, xylan, andcyclodextrins. Prebiotics may also be purified or chemically orenzymatically synthesized.

Production of PhABs

In certain aspects, the PhABs described herein can be prepared using anymethod known in the art.

In some embodiments, the PhABs described herein are prepared byfractionation. Bacterial cells and/or supernatants from culturedbacteria cells are fractionated into various pharmacologically activebiomass (PhABs) and/or products derived therefrom. Bacterial cellsand/or supernatants are fractionated using materials and methods knownin the art (see e.g. Sandrini et al. Fractionation byultracentrifugation of gram negative cytoplasmic and membrane proteins.2014. Bio-Protocol. 4(21); Scholler et al. Protoplast and cytoplasmicmembrane preparations from Streptococcus sanguis and Streptococcusmutans. 1983. J Gen Micro. 129: 3271-3279; Thein et al. Efficientsubfractionation of gram-negative bacteria for proteomics studies. 2010.Am Chem Society. 9: 6135-6147; Hobb et al. Evaluation of procedures forouter membrane isolation from Campylobacter jejuni. 2009. 155(Pt. 3):979-988).

Additionally, PhABs obtained by methods provided herein may be furtherpurified by size based column chromatography, by affinitychromatography, and by gradient ultracentrifugation, using methods thatmay include, but are not limited to, use of a sucrose gradient orOptiprep gradient. Briefly, using a sucrose gradient method, if ammoniumsulfate precipitation or ultracentrifugation were used to concentratethe filtered supernatants, pellets are resuspended in 60% sucrose, 30 mMTris, pH 8.0. If filtration was used to concentrate the filteredsupernatant, the concentrate is buffer exchanged into 60% sucrose, 30 mMTris, pH 8.0, using an Amicon Ultra column. Samples are applied to a35-60% discontinuous sucrose gradient and centrifuged at 200,000×g for3-24 hours at 4° C. Briefly, using an Optiprep gradient method, ifammonium sulfate precipitation or ultracentrifugation were used toconcentrate the filtered supernatants, pellets are resuspended in 35%Optiprep in PBS. In some embodiments, if filtration was used toconcentrate the filtered supernatant, the concentrate is diluted using60% Optiprep to a final concentration of 35% Optiprep. Samples areapplied to a 35-60% discontinuous sucrose gradient and centrifuged at200,000×g for 3-24 hours at 4° C.

In some embodiments, to confirm sterility and isolation of the PhABpreparations, PhABs are serially diluted onto agar medium used forroutine culture of the bacteria being tested, and incubated usingroutine conditions. Non-sterile preparations are passed through a 0.22um filter to exclude intact cells. To further increase purity, isolatedPhABs may be DNase or proteinase K treated.

In some embodiments, for preparation of PhABs used for in vivoinjections, purified PhABs are processed as described previously (G.Norheim, et al. PLoS ONE. 10(9): e0134353 (2015)). Briefly, aftersucrose gradient centrifugation, bands containing PhABs are resuspendedto a final concentration of 50 μg/mL in a solution containing 3% sucroseor other solution suitable for in vivo injection known to one skilled inthe art. This solution may also contain adjuvant, for example aluminumhydroxide at a concentration of 0-0.5% (w/v).

In certain embodiments, to make samples compatible with further testing(e.g. to remove sucrose prior to TEM imaging or in vitro assays),samples are buffer exchanged into PBS or 30 mM Tris, pH 8.0 usingfiltration (e.g. Amicon Ultra columns), dialysis, or ultracentrifugation(200,000×g, ≥3 hours, 4° C.) and resuspension.

In some embodiments, the sterility of the PhAB preparations can beconfirmed by plating a portion of the PhABs onto agar medium used forstandard culture of the bacteria used in the generation of the PhABs andincubating using standard conditions.

In some embodiments select PhABs are isolated and enriched bychromatography and binding surface moieties on PhABs. In otherembodiments, select PhABs are isolated and/or enriched by fluorescentcell sorting by methods using affinity reagents, chemical dyes,recombinant proteins or other methods known to one skilled in the art.

Administration

In certain aspects, provided herein is a method of delivering abacterium and/or a bacterial composition described herein to a subject.In some embodiments of the methods provided herein, the bacteria areadministered in conjunction with the administration of a cancertherapeutic. In some embodiments, the bacteria is co-formulated in apharmaceutical composition with the cancer therapeutic. In someembodiments, the bacteria is co-administered with the cancertherapeutic. In some embodiments, the cancer therapeutic is administeredto the subject before administration of the bacteria (e.g., about 1, 2,3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40, 45, 50 or 55 minutesbefore, about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17,18, 19, 20, 21, 22 or 23 hours before, or about 1, 2, 3, 4, 5, 6, 7, 8,9, 10, 11, 12, 13 or 14 days before). In some embodiments, the cancertherapeutic is administered to the subject after administration of thebacteria (e.g., about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35,40, 45, 50 or 55 minutes after, about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11,12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22 or 23 hours after, or about1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13 or 14 days after). In someembodiments, the same mode of delivery is used to deliver both thebacteria and the cancer therapeutic. In some embodiments different modesof delivery are used to administer the bacteria and the cancertherapeutic. For example, in some embodiments, the bacteria isadministered orally while the cancer therapeutic is administered viainjection (e.g., an intravenious, intramuscular and/or intratumoralinjection).

In certain embodiments, the pharmaceutical compositions, dosage forms,and kits described herein can be administered in conjunction with anyother conventional anti-cancer treatment, such as, for example,radiation therapy and surgical resection of the tumor. These treatmentsmay be applied as necessary and/or as indicated and may occur before,concurrent with or after administration of the pharmaceuticalcompositions, dosage forms, and kits described herein.

The dosage regimen can be any of a variety of methods and amounts, andcan be determined by one skilled in the art according to known clinicalfactors. As is known in the medical arts, dosages for any one patientcan depend on many factors, including the subject's species, size, bodysurface area, age, sex, immunocompetence, and general health, theparticular microorganism to be administered, duration and route ofadministration, the kind and stage of the disease, for example, tumorsize, and other compounds such as drugs being administered concurrently.In addition to the above factors, such levels can be affected by theinfectivity of the microorganism, and the nature of the microorganism,as can be determined by one skilled in the art. In the present methods,appropriate minimum dosage levels of microorganisms can be levelssufficient for the microorganism to survive, grow and replicate in atumor or metastasis. The methods of treatment described herein may besuitable for the treatment of a primary tumor, a secondary tumor ormetastasis, as well as for recurring tumors or cancers. The dose of thepharmaceutical compositions described herein may be appropriately set oradjusted in accordance with the dosage form, the route ofadministration, the degree or stage of a target disease, and the like.For example, the general effective dose of the agents may range between0.01 mg/kg body weight/day and 1000 mg/kg body weight/day, between 0.1mg/kg body weight/day and 1000 mg/kg body weight/day, 0.5 mg/kg bodyweight/day and 500 mg/kg body weight/day, 1 mg/kg body weight/day and100 mg/kg body weight/day, or between 5 mg/kg body weight/day and 50mg/kg body weight/day. The effective dose may be 0.01, 0.05, 0.1, 0.5,1, 2, 3, 5, 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 200, 500, or 1000mg/kg body weight/day or more, but the dose is not limited thereto.

In some embodiments, the dose administered to a subject is sufficient toprevent cancer, delay its onset, or slow or stop its progression orprevent a relapse of a cancer. One skilled in the art will recognizethat dosage will depend upon a variety of factors including the strengthof the particular compound employed, as well as the age, species,condition, and body weight of the subject. The size of the dose willalso be determined by the route, timing, and frequency of administrationas well as the existence, nature, and extent of any adverse side-effectsthat might accompany the administration of a particular compound and thedesired physiological effect.

Suitable doses and dosage regimens can be determined by conventionalrange-finding techniques known to those of ordinary skill in the art.Generally, treatment is initiated with smaller dosages, which are lessthan the optimum dose of the compound. Thereafter, the dosage isincreased by small increments until the optimum effect under thecircumstances is reached. An effective dosage and treatment protocol canbe determined by routine and conventional means, starting e.g., with alow dose in laboratory animals and then increasing the dosage whilemonitoring the effects, and systematically varying the dosage regimen aswell. Animal studies are commonly used to determine the maximaltolerable dose (“MTD”) of bioactive agent per kilogram weight. Thoseskilled in the art regularly extrapolate doses for efficacy, whileavoiding toxicity, in other species, including humans.

In accordance with the above, in therapeutic applications, the dosagesof the active agents used in accordance with the invention varydepending on the active agent, the age, weight, and clinical conditionof the recipient patient, and the experience and judgment of theclinician or practitioner administering the therapy, among other factorsaffecting the selected dosage. Generally, the dose should be sufficientto result in slowing, and preferably regressing, the growth of thetumors and most preferably causing complete regression of the cancer.

Separate administrations can include any number of two or moreadministrations (e.g., doses), including two, three, four, five or sixadministrations. One skilled in the art can readily determine the numberof administrations to perform, or the desirability of performing one ormore additional administrations, according to methods known in the artfor monitoring therapeutic methods and other monitoring methods providedherein. In some embodiments, the doses may be separated by at least 1,2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21,22, 23, 24, 25, 26, 27, 28, 29 or 30 days or 1, 2, 3, or 4 weeks.Accordingly, the methods provided herein include methods of providing tothe subject one or more administrations of a bacterium, where the numberof administrations can be determined by monitoring the subject, and,based on the results of the monitoring, determining whether or not toprovide one or more additional administrations. Deciding on whether ornot to provide one or more additional administrations can be based on avariety of monitoring results, including, but not limited to, indicationof tumor growth or inhibition of tumor growth, appearance of newmetastases or inhibition of metastasis, the subject's anti-bacteriumantibody titer, the subject's anti-tumor antibody titer, the overallhealth of the subject and/or the weight of the subject.

The time period between administrations can be any of a variety of timeperiods. The time period between administrations can be a function ofany of a variety of factors, including monitoring steps, as described inrelation to the number of administrations, the time period for a subjectto mount an immune response and/or the time period for a subject toclear the bacteria from normal tissue. In one example, the time periodcan be a function of the time period for a subject to mount an immuneresponse; for example, the time period can be more than the time periodfor a subject to mount an immune response, such as more than about oneweek, more than about ten days, more than about two weeks, or more thanabout a month; in another example, the time period can be less than thetime period for a subject to mount an immune response, such as less thanabout one week, less than about ten days, less than about two weeks, orless than about a month. In another example, the time period can be afunction of the time period for a subject to clear the bacteria fromnormal tissue; for example, the time period can be more than the timeperiod for a subject to clear the bacteria from normal tissue, such asmore than about a day, more than about two days, more than about threedays, more than about five days, or more than about a week.

In some embodiments, the delivery of a cancer therapeutic in combinationwith the bacteria described herein reduces the adverse effects and/orimproves the efficacy of the cancer therapeutic.

The effective dose of a cancer therapeutic described herein is theamount of the therapeutic agent that is effective to achieve the desiredtherapeutic response for a particular patient, composition, and mode ofadministration, with the least toxicity to the patient. The effectivedosage level can be identified using the methods described herein andwill depend upon a variety of pharmacokinetic factors including theactivity of the particular compositions administered, the route ofadministration, the time of administration, the rate of excretion of theparticular compound being employed, the duration of the treatment, otherdrugs, compounds and/or materials used in combination with theparticular compositions employed, the age, sex, weight, condition,general health and prior medical history of the patient being treated,and like factors well known in the medical arts. In general, aneffective dose of a cancer therapy will be the amount of the therapeuticagent which is the lowest dose effective to produce a therapeuticeffect. Such an effective dose will generally depend upon the factorsdescribed above.

The toxicity of a cancer therapy is the level of adverse effectsexperienced by the subject during and following treatment. Adverseevents associated with cancer therapy toxicity include, but are notlimited to, abdominal pain, acid indigestion, acid reflux, allergicreactions, alopecia, anaphylaxis, anemia, anxiety, lack of appetite,arthralgias, asthenia, ataxia, azotemia, loss of balance, bone pain,bleeding, blood clots, low blood pressure, elevated blood pressure,difficulty breathing, bronchitis, bruising, low white blood cell count,low red blood cell count, low platelet count, cardiotoxicity, cystitis,hemorrhagic cystitis, arrhythmias, heart valve disease, cardiomyopathy,coronary artery disease, cataracts, central neurotoxicity, cognitiveimpairment, confusion, conjunctivitis, constipation, coughing, cramping,cystitis, deep vein thrombosis, dehydration, depression, diarrhea,dizziness, dry mouth, dry skin, dyspepsia, dyspnea, edema, electrolyteimbalance, esophagitis, fatigue, loss of fertility, fever, flatulence,flushing, gastric reflux, gastroesophageal reflux disease, genital pain,granulocytopenia, gynecomastia, glaucoma, hair loss, hand-foot syndrome,headache, hearing loss, heart failure, heart palpitations, heartburn,hematoma, hemorrhagic cystitis, hepatotoxicity, hyperamylasemia,hypercalcemia, hyperchloremia, hyperglycemia, hyperkalemia,hyperlipasemia, hypermagnesemia, hypernatremia, hyperphosphatemia,hyperpigmentation, hypertriglyceridemia, hyperuricemia, hypoalbuminemia,hypocalcemia, hypochloremia, hypoglycemia, hypokalemia, hypomagnesemia,hyponatremia, hypophosphatemia, impotence, infection, injection sitereactions, insomnia, iron deficiency, itching, joint pain, kidneyfailure, leukopenia, liver dysfunction, memory loss, menopause, mouthsores, mucositis, muscle pain, myalgias, myelosuppression, myocarditis,neutropenic fever, nausea, nephrotoxicity, neutropenia, nosebleeds,numbness, ototoxicity, pain, palmar-plantar erythrodysesthesia,pancytopenia, pericarditis, peripheral neuropathy, pharyngitis,photophobia, photosensitivity, pneumonia, pneumonitis, proteinuria,pulmonary embolus, pulmonary fibrosis, pulmonary toxicity, rash, rapidheart beat, rectal bleeding, restlessness, rhinitis, seizures, shortnessof breath, sinusitis, thrombocytopenia, tinnitus, urinary tractinfection, vaginal bleeding, vaginal dryness, vertigo, water retention,weakness, weight loss, weight gain, and xerostomia. In general, toxicityis acceptable if the benefits to the subject achieved through thetherapy outweigh the adverse events experienced by the subject due tothe therapy.

In some embodiments, the administration of the bacterial compositiontreats the cancer. In some embodiments, the bacterial compositioninduces an anti-tumor immune response in the subject.

Therapeutic Agents

In certain aspects, the methods provided herein include theadministration to a subject of a bacterium and/or a bacterialcomposition described herein (e.g., a Bifidobacterium animalis ssp.Lactis-containing bacterial composition) either alone or in combinationwith another cancer therapeutic. The other cancer therapeutic mayinclude e.g., surgical resection, radiotherapy, or a cancer therapeuticagent. In some embodiments, the bacterial composition and the othercancer therapy can be administered to the subject in any order. In someembodiments, the bacterial composition and the other cancer therapy areadministered conjointly.

In some embodiments the bacterium is administered to the subject beforethe cancer therapeutic is administered (e.g., at least 1, 2, 3, 4, 5, 6,7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23 or 24hours before or at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14,15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29 or 30 daysbefore). In some embodiments the bacterium is administered to thesubject after the cancer therapeutic is administered (e.g., at least 1,2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21,22, 23 or 24 hours after or at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11,12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29or 30 days after). In some embodiments, the bacterium and the cancertherapeutic are administered to the subject simultaneously or nearlysimultaneously (e.g., administrations occur within an hour of eachother). In some embodiments, the subject is administered an antibioticbefore the bacterium is administered to the subject (e.g., at least 1,2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21,22, 23 or 24 hours before or at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11,12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29or 30 days before),In some embodiments, the subject is administered anantibiotic after the bacterium is administered to the subject (e.g., atleast 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19,20, 21, 22, 23 or 24 hours before or at least 1, 2, 3, 4, 5, 6, 7, 8, 9,10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27,28, 29 or 30 days after). In some embodiments, the bacterium and theantibiotic are administered to the subject simultaneously or nearlysimultaneously (e.g., administrations occur within an hour of eachother).

In certain embodiments, the subject may undergo surgery. Types ofsurgery include but are not limited to preventative, diagnostic orstaging, curative and palliative surgery. Curative surgery is a cancertreatment that may be used in conjunction with other therapies, such asthe treatment of the present invention, chemotherapy, radiotherapy,hormonal therapy, gene therapy, immunotherapy and/or alternativetherapies.

Curative surgery includes resection in which all or part of canceroustissue is physically removed, excised, and/or destroyed. Tumor resectionrefers to physical removal of at least part of a tumor. In addition totumor resection, treatment by surgery includes laser surgery,cryosurgery, electrosurgery, and microscopically controlled surgery(Mohs' surgery). Upon excision of part of all of cancerous cells,tissue, or tumor, a cavity may be formed in the body.

In certain embodiments, the subject may undergo radiation therapy.Radiation therapy includes the administration or application of aradiotherapeutic agents and factors including but not limited to Inaddition to trays, UV-irradiation, microwaves, electronic emissions, andradioisotopes. The localized tumor site may be irradiated, including byone or more the above described forms of radiations. All of thesefactors may effect a broad range of damage DNA, on the precursors ofDNA, the replication and repair of DNA, and the assembly and maintenanceof chromosomes.

Dosage ranges for X-rays range from daily doses of 50 to 200 roentgensfor prolonged periods of time (3 to 4 weeks), to single doses of 2000 to6000 roentgens. Dosage ranges for radioisotopes vary widely, and dependon the half-life of the isotope, the strength and type of radiationemitted, and the uptake by the neoplastic cells.

In certain aspects, the methods provided herein further compriseadministering another cancer therapeutic to the subject.

In some embodiments, the cancer therapeutic is a chemotherapeutic agent.Examples of such chemotherapeutic agents include, but are not limitedto, alkylating agents such as thiotepa and cyclosphosphamide; alkylsulfonates such as busulfan, improsulfan and piposulfan; aziridines suchas benzodopa, carboquone, meturedopa, and uredopa; ethylenimines andmethylamelamines including altretamine, triethylenemelamine,trietylenephosphoramide, triethiylenethiophosphoramide andtrimethylolomelamine; acetogenins (especially bullatacin andbullatacinone); a camptothecin (including the synthetic analoguetopotecan); bryostatin; callystatin; CC-1065 (including its adozelesin,carzelesin and bizelesin synthetic analogues); cryptophycins(particularly cryptophycin 1 and cryptophycin 8); dolastatin;duocarmycin (including the synthetic analogues, KW-2189 and CB1-TM1);eleutherobin; pancratistatin; a sarcodictyin; spongistatin; nitrogenmustards such as chlorambucil, chlornaphazine, cholophosphamide,estramustine, ifosfamide, mechlorethamine, mechlorethamine oxidehydrochloride, melphalan, novembichin, phenesterine, prednimustine,trofosfamide, uracil mustard; nitrosureas such as carmustine,chlorozotocin, fotemustine, lomustine, nimustine, and ranimnustine;antibiotics such as the enediyne antibiotics (e.g., calicheamicin,especially calicheamicin gammalI and calicheamicin omegal1; dynemicin,including dynemicin A; bisphosphonates, such as clodronate; anesperamicin; as well as neocarzinostatin chromophore and relatedchromoprotein enediyne antibiotic chromophores, aclacinomysins,actinomycin, authrarnycin, azaserine, bleomycins, cactinomycin,carabicin, caminomycin, carzinophilin, chromomycinis, dactinomycin,daunorubicin, detorubicin, 6-diazo-5-oxo-L-norleucine, doxorubicin(including morpholino-doxorubicin, cyanomorpholino-doxorubicin,2-pyrrolino-doxorubicin and deoxydoxorubicin), epirubicin, esorubicin,idarubicin, marcellomycin, mitomycins such as mitomycin C, mycophenolicacid, nogalamycin, olivomycins, peplomycin, potfiromycin, puromycin,quelamycin, rodorubicin, streptonigrin, streptozocin, tubercidin,ubenimex, zinostatin, zorubicin; anti-metabolites such as methotrexateand 5-fluorouracil (5-FU); folic acid analogues such as denopterin,methotrexate, pteropterin, trimetrexate; purine analogs such asfludarabine, 6-mercaptopurine, thiamiprine, thioguanine; pyrimidineanalogs such as ancitabine, azacitidine, 6-azauridine, carmofur,cytarabine, dideoxyuridine, doxifluridine, enocitabine, floxuridine;androgens such as calusterone, dromostanolone propionate, epitiostanol,mepitiostane, testolactone; anti-adrenals such as aminoglutethimide,mitotane, trilostane; folic acid replenisher such as frolinic acid;aceglatone; aldophosphamide glycoside; aminolevulinic acid; eniluracil;amsacrine; bestrabucil; bisantrene; edatraxate; defofamine; demecolcine;diaziquone; elformithine; elliptinium acetate; an epothilone; etoglucid;gallium nitrate; hydroxyurea; lentinan; lonidainine; maytansinoids suchas maytansine and ansamitocins; mitoguazone; mitoxantrone; mopidanmol;nitraerine; pentostatin; phenamet; pirarubicin; losoxantrone;podophyllinic acid; 2-ethylhydrazide; procarbazine; PSK polysaccharidecomplex); razoxane; rhizoxin; sizofuran; spirogermanium; tenuazonicacid; triaziquone; 2,2′,2″-trichlorotriethylamine; trichothecenes(especially T-2 toxin, verracurin A, roridin A and anguidine); urethan;vindesine; dacarbazine; mannomustine; mitobronitol; mitolactol;pipobroman; gacytosine; arabinoside (“Ara-C”); cyclophosphamide;thiotepa; taxoids, e.g., paclitaxel and doxetaxel; chlorambucil;gemcitabine; 6-thioguanine; mercaptopurine; methotrexate; platinumcoordination complexes such as cisplatin, oxaliplatin and carboplatin;vinblastine; platinum; etoposide (VP-16); ifosfamide; mitoxantrone;vincristine; vinorelbine; novantrone; teniposide; edatrexate;daunomycin; aminopterin; xeloda; ibandronate; irinotecan (e.g., CPT-11);topoisomerase inhibitor RFS 2000; difluoromethylomithine (DMFO);retinoids such as retinoic acid; capecitabine; and pharmaceuticallyacceptable salts, acids or derivatives of any of the above.

In some embodiments, the cancer therapeutic is a cancer immunotherapyagent. Immunotherapy refers to a treatment that uses a subject's immunesystem to treat cancer, e.g., checkpoint inhibitors, cancer vaccines,cytokines, cell therapy, CAR-T cells, and dendritic cell therapy.Non-limiting examples of immunotherapies are checkpoint inhibitorsinclude Nivolumab (BMS, anti-PD-1), Pembrolizumab (Merck, anti-PD-1),Ipilimumab (BMS, anti-CTLA-4), MEDI4736 (Astra7eneca, anti-PD-L1), andMPDL3280A (Roche, anti-PD-L1). Other immunotherapies may be tumorvaccines, such as Gardail, Cervarix, BCG, sipulencel-T, Gp100:209-217,AGS-003, DCVax-L, Algenpantucel-L, Tergenpantucel-L, TG4010, ProstAtak,Prostvac-V/R-TRICOM, Rindopepimul, E75 peptide acetate, IMA901,POL-103A, Belagenpumatucel-L, GSK1572932A, MDX-1279, GV1001, andTecemotide. Immunotherapy may be administered via injection (e.g.,intravenously, intratumorally, subcutaneously, or into lymph nodes), butmay also be administered orally, topically, or via aerosol.Immunotherapies may comprise adjuvants such as cytokines.

In some embodiments, the immunotherapy agent is an immune checkpointinhibitor. Immune checkpoint inhibition broadly refers to inhibiting thecheckpoints that cancer cells can produce to prevent or downregulate animmune response. Examples of immune checkpoint proteins include, but arenot limited to, CTLA4, PD-1, PD-L1, PD-L2, A2AR, B7-H3, B7-H4, BTLA,KIR, LAGS, TIM-3 or VISTA. Immune checkpoint inhibitors can beantibodies or antigen binding fragments thereof that bind to and inhibitan immune checkpoint protein. Examples of immune checkpoint inhibitorsinclude, but are not limited to, nivolumab, pembrolizumab, pidilizumab,AMP-224, AMP-514, STI-A1110, TSR-042, RG-7446, BMS-936559, MEDI-4736,MSB-0020718C, AUR-012 and STI-A1010. In some embodiments, the cancerimmunotherapy includes administering an additional immune checkpointinhibitor (e.g., administering 2, 3, 4, or 5, immune checkpointinhibitors) to the subject

In certain embodiments, immune checkpoint inhibitors can be aninhibitory nucleic acid molecule (e.g., an siRNA molecule, an shRNAmolecule or an antisense RNA molecule) that inhibits expression fo animmune checkpoint protein that inhibits expression of an immunecheckpoint protein.

In some embodiments, the immune checkpoint inhibitor is a siRNAmolecule. Such siRNA molecules should include a region of sufficienthomology to the target region, and be of sufficient length in terms ofnucleotides, such that the siRNA molecule down-regulate target RNA(e.g., RNA of an immune checkpoint protein). The term “ribonucleotide”or “nucleotide” can, in the case of a modified RNA or nucleotidesurrogate, also refer to a modified nucleotide, or surrogate replacementmoiety at one or more positions. It is not necessary that there beperfect complementarity between the siRNA molecule and the target, butthe correspondence must be sufficient to enable the siRNA molecule todirect sequence-specific silencing, such as by RNAi cleavage of thetarget RNA. In some embodiments, the sense strand need only besufficiently complementary with the antisense strand to maintain theoverall double-strand character of the molecule.

In addition, an siRNA molecule may be modified or include nucleosidesurrogates. Single stranded regions of an siRNA molecule may be modifiedor include nucleoside surrogates, e.g., the unpaired region or regionsof a hairpin structure, e.g., a region which links two complementaryregions, can have modifications or nucleoside surrogates. Modificationto stabilize one or more 3′- or 5′-terminus of an siRNA molecule, e.g.,against exonucleases, or to favor the antisense siRNA agent to enterinto RISC are also useful. Modifications can include C3 (or C6, C7, C12)amino linkers, thiol linkers, carboxyl linkers, non-nucleotidic spacers(C3, C6, C9, C12, abasic, triethylene glycol, hexaethylene glycol),special biotin or fluorescein reagents that come as phosphoramidites andthat have another DMT-protected hydroxyl group, allowing multiplecouplings during RNA synthesis.

Each strand of an siRNA molecule can be equal to or less than 35, 30,25, 24, 23, 22, 21, or 20 nucleotides in length. In some embodiments,the strand is at least 19 nucleotides in length. For example, eachstrand can be between 21 and 25 nucleotides in length. In someembodiments, siRNA agents have a duplex region of 17, 18, 19, 29, 21,22, 23, 24, or 25 nucleotide pairs, and one or more overhangs, such asone or two 3′ overhangs, of 2-3 nucleotides.

In some embodiments, the immune checkpoint inhibitor is a shRNAmolecule. A “small hairpin RNA” or “short hairpin RNA” or “shRNA”includes a short RNA sequence that makes a tight hairpin turn that canbe used to silence gene expression via RNA interference. The shRNAsprovided herein may be chemically synthesized or transcribed from atranscriptional cassette in a DNA plasmid. The shRNA hairpin structureis cleaved by the cellular machinery into siRNA, which is then bound tothe RNA-induced silencing complex (RISC).

In some embodiments, shRNAs are about 15-60, 15-50, or 15-40 (duplex)nucleotides in length, about 15-30, 15-25, or 19-25 (duplex) nucleotidesin length, or are about 20-24, 21-22, or 21-23 (duplex) nucleotides inlength (e.g., each complementary sequence of the double-stranded shRNAis 15-60, 15-50, 15-40, 15-30, 15-25, or 19-25 nucleotides in length, orabout 20-24, 21-22, or 21-23 nucleotides in length, and thedouble-stranded shRNA is about 15-60, 15-50, 15-40, 15-30, 15-25, or19-25 base pairs in length, or about 18-22, 19-20, or 19-21 base pairsin length). shRNA duplexes may comprise 3′ overhangs of about 1 to about4 nucleotides or about 2 to about 3 nucleotides on the antisense strandand/or 5′-phosphate termini on the sense strand. In some embodiments,the shRNA comprises a sense strand and/or antisense strand sequence offrom about 15 to about 60 nucleotides in length (e.g., about 15-60,15-55, 15-50, 15-45, 15-40, 15-35, 15-30, or 15-25 nucleotides inlength), or from about 19 to about 40 nucleotides in length (e.g., about19-40, 19-35, 19-30, or 19-25 nucleotides in length), or from about 19to about 23 nucleotides in length (e.g., 19, 20, 21, 22, or 23nucleotides in length).

Non-limiting examples of shRNA include a double-stranded polynucleotidemolecule assembled from a single-stranded molecule, where the sense andantisense regions are linked by a nucleic acid-based or non-nucleicacid-based linker; and a double-stranded polynucleotide molecule with ahairpin secondary structure having self-complementary sense andantisense regions. In some embodiments, the sense and antisense strandsof the shRNA are linked by a loop structure comprising from about 1 toabout 25 nucleotides, from about 2 to about 20 nucleotides, from about 4to about 15 nucleotides, from about 5 to about 12 nucleotides, or 1, 2,3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22,23, 24, 25, or more nucleotides.

Additional embodiments related to the shRNAs, as well as methods ofdesigning and synthesizing such shRNAs, are described in U.S. patentapplication publication number 2011/0071208, the disclosure of which isherein incorporated by reference in its entirety for all purposes.

In some embodiments, the immune checkpoint inhibitor is an antisenseoligonucleotide compounds that inhbits expression of an immunecheckpoint protein. In certain embodiments, the degree ofcomplementarity between the target sequence and antisense targetingsequence is sufficient to form a stable duplex. The region ofcomplementarity of the antisense oligonucleotides with the target RNAsequence may be as short as 8-11 bases, but can be 12-15 bases or more,e.g., 10-40 bases, 12-30 bases, 12-25 bases, 15-25 bases, 12-20 bases,or 15-20 bases, including all integers in between these ranges. Anantisense oligonucleotide of about 14-15 bases is generally long enoughto have a unique complementary sequence.

In certain embodiments, antisense oligonucleotides may be 100%complementary to the target sequence, or may include mismatches, e.g.,to improve selective targeting of allele containing thedisease-associated mutation, as long as a heteroduplex formed betweenthe oligonucleotide and target sequence is sufficiently stable towithstand the action of cellular nucleases and other modes ofdegradation which may occur in vivo. Hence, certain oligonucleotides mayhave about or at least about 70% sequence complementarity, e.g., 70%,71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%,85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%,99% or 100% sequence complementarity, between the oligonucleotide andthe target sequence. Oligonucleotide backbones that are less susceptibleto cleavage by nucleases are discussed herein. Mismatches, if present,are typically less destabilizing toward the end regions of the hybridduplex than in the middle. The number of mismatches allowed will dependon the length of the oligonucleotide, the percentage of G:C base pairsin the duplex, and the position of the mismatch(es) in the duplex,according to well understood principles of duplex stability.

The inhibitory nucleic acid molecule can be prepared, for example, bychemical synthesis, in vitro transcription, or digestion of long dsRNAby Rnase III or Dicer. These can be introduced into cells bytransfection, electroporation, or other methods known in the art. SeeHannon, G J, 2002, RNA Interference, Nature 418: 244-251; Bernstein E etal., 2002, The rest is silence. RNA 7: 1509-1521; Hutvagner G et al.,RNAi: Nature abhors a double-strand. Curr. Opin. Genetics & Development12: 225-232; Brummelkamp, 2002, A system for stable expression of shortinterfering RNAs in mammalian cells. Science 296: 550-553; Lee N S,Dohjima T, Bauer G, Li H, Li M-J, Ehsani A, Salvaterra P, and Rossi J.(2002). Expression of small interfering RNAs targeted against HIV-1 revtranscripts in human cells. Nature Biotechnol. 20:500-505; Miyagishi M,and Taira K. (2002). U6-promoter-driven siRNAs with four uridine 3′overhangs efficiently suppress targeted gene expression in mammaliancells. Nature Biotechnol. 20:497-500; Paddison P J, Caudy A A, BernsteinE, Hannon G J, and Conklin D S. (2002). Short hairpin RNAs (shRNAs)induce sequence-specific silencing in mammalian cells. Genes & Dev.16:948-958; Paul C P, Good P D, Winer I, and Engelke D R. (2002).Effective expression of small interfering RNA in human cells. NatureBiotechnol. 20:505-508; Sui G, Soohoo C, Affar E-B, Gay F, Shi Y,Forrester W C, and Shi Y. (2002). A DNA vector-based RNAi technology tosuppress gene expression in mammalian cells. Proc. Natl. Acad. Sci. USA99(6):5515-5520; Yu J-Y, DeRuiter S L, and Turner D L. (2002). RNAinterference by expression of short-interfering RNAs and hairpin RNAs inmammalian cells. Proc. Natl. Acad. Sci. USA 99(9):6047-6052.

In the present methods, the inhibitory nucleic acid molecule can beadministered to the subject, for example, as naked nucleic acid, incombination with a delivery reagent, and/or as a nucleic acid comprisingsequences that express an interfering nucleic acid molecule. In someembodiments the nucleic acid comprising sequences that express theinterfering nucleic acid molecules are delivered within vectors, e.g.plasmid, viral and bacterial vectors. Any nucleic acid delivery methodknown in the art can be used in the methods described herein. Suitabledelivery reagents include, but are not limited to, e.g., the MirusTransit TKO lipophilic reagent; lipofectin; lipofectamine; cellfectin;polycations (e.g., polylysine), atelocollagen, nanoplexes and liposomes.The use of atelocollagen as a delivery vehicle for nucleic acidmolecules is described in Minakuchi et al. Nucleic Acids Res.,32(13):e109 (2004); Hanai et al. Ann NY Acad Sci., 1082:9-17 (2006); andKawata et al. Mol Cancer Ther., 7(9):2904-12 (2008); each of which isincorporated herein in their entirety. Exemplary interfering nucleicacid delivery systems are provided in U.S. Pat. Nos. 8,283,461,8,313,772, 8,501,930. 8,426,554, 8,268,798 and 8,324,366, each of whichis hereby incorporated by reference in its entirety.

In some embodiments, the immunotherapy agent is an antibody or antigenbinding fragment thereof that, for example, binds to a cancer-associatedantigen. Examples of cancer-associated antigens include, but are notlimited to, adipophilin, AIM-2, ALDH1A1, alpha-actinin-4,alpha-fetoprotein (“AFP”), ARTC1, B-RAF, BAGE-1, BCLX (L), BCR-ABLfusion protein b3a2, beta-catenin, BING-4, CA-125, CALCA,carcinoembryonic antigen (“CEA”), CASP-5, CASP-8, CD274, CD45, Cdc27,CDK12, CDK4, CDKN2A, CEA, CLPP, COA-1, CPSF, CSNK1A1, CTAG1, CTAG2,cyclin D1, Cyclin-A1, dek-can fusion protein, DKK1, EFTUD2, Elongationfactor 2, ENAH (hMena), Ep-CAM, EpCAM, EphA3, epithelial tumor antigen(“ETA”), ETV6-AML1 fusion protein, EZH2, FGF5, FLT3-ITD, FN1,G250/MN/CAIX, GAGE-1,2,8, GAGE-3,4,5,6,7, GAS7, glypican-3, GnTV,gp100/Pmel17, GPNMB, HAUS3, Hepsin, HER-2/neu, HERV-K-MEL, HLA-A11,HLA-A2, HLA-DOB, hsp70-2, IDO1, IGF2B3, IL13Ralpha2, Intestinal carboxylesterase, K-ras, Kallikrein 4, KIF20A, KK-LC-1, KKLC1, KM-HN-1, KMHN1also known as CCDC110, LAGE-1, LDLR-fucosyltransferaseAS fusion protein,Lengsin, M-CSF, MAGE-A1, MAGE-A10, MAGE-A12, MAGE-A2, MAGE-A3, MAGE-A4,MAGE-A6, MAGE-A9, MAGE-C1, MAGE-C2, malic enzyme, mammaglobin-A, MART2,MATN, MC1R, MCSP, mdm-2, ME1, Melan-A/MART-1, Meloe, Midkine, MMP-2,MMP-7, MUC1, MUCSAC, mucin, MUM-1, MUM-2, MUM-3, Myosin, Myosin class I,N-raw, NA88-A, neo-PAP, NFYC, NY-BR-1, NY-ESO-1/LAGE-2, OA1, OGT, OS-9,P polypeptide, p53, PAP, PAXS, PBF, pml-RARalpha fusion protein,polymorphic epithelial mucin (“PEM”), PPP1R3B, PRAME, PRDXS, PSA, PSMA,PTPRK, RAB38/NY-MEL-1, RAGE-1, RBAF600, RGS5, RhoC, RNF43, RU2AS, SAGE,secernin 1, SIRT2, SNRPD1, SOX10, Sp17, SPA17, SSX-2, SSX-4, STEAP1,survivin, SYT-SSX1 or -SSX2 fusion protein, TAG-1, TAG-2, Telomerase,TGF-betaRII, TPBG, TRAG-3, Triosephosphate isomerase, TRP-1/gp75, TRP-2,TRP2-INT2, tyrosinase, tyrosinase (“TYR”), VEGF, WT1, XAGE-1b/GAGED2a.In some embodiments, the antigen is a neo-antigen.

In some embodiments, the immunotherapy agent is a cancer vaccine and/ora component of a cancer vaccine (e.g., an antigenic peptide and/orprotein). The cancer vaccine can be a protein vaccine, a nucleic acidvaccine or a combination thereof. For example, in some embodiments, thecancer vaccine comprises a polypeptide comprising an epitope of acancer-associated antigen. In some embodiments, the cancer vaccinecomprises a nucleic acid (e.g., DNA or RNA, such as mRNA) that encodesan epitope of a cancer-associated antigen. In some embodiemnts, thenucleic acid is a vector (e.g., a bacterial vector, viral vector).Examples of bacterial vectors include, but are not limited to,Mycobacterium bovis (BCG), Salmonella Typhimurium ssp., Salmonella Typhissp., Clostridium sp. spores, Escherichia coli Nissle 1917, Escherichiacoli K-12/LLO, Listeria monocytogenes, and Shigella flexneri. Examplesof viral vectors include, but are not limited to, vaccinia, adenovirus,RNA viruses, and replication-defective avipox, replication-defectivefowlpox, replication-defective canarypox, replication-defective MVA andreplication-defective adenovirus.

In some embodiments, the cancer immunotherapy comprises administrationof an antigen presenting cell (APC) primed with a cancer-specificantigen. In some embodiments, the APC is a dendritic cell, a macrophageor a B cell.

Examples of cancer-associated antigens include, but are not limited to,adipophilin, AIM-2, ALDH1A1, alpha-actinin-4, alpha-fetoprotein (“AFP”),ARTC1, B-RAF, BAGE-1, BCLX (L), BCR-ABL fusion protein b3a2,beta-catenin, BING-4, CA-125, CALCA, carcinoembryonic antigen (“CEA”),CASP-5, CASP-8, CD274, CD45, Cdc27, CDK12, CDK4, CDKN2A, CEA, CLPP,COA-1, CPSF, CSNK1A1, CTAG1, CTAG2, cyclin D1, Cyclin-A1, dek-can fusionprotein, DKK1, EFTUD2, Elongation factor 2, ENAH (hMena), Ep-CAM, EpCAM,EphA3, epithelial tumor antigen (“ETA”), ETV6-AML1 fusion protein, EZH2,FGF5, FLT3-ITD, FN1, G250/MN/CAIX, GAGE-1,2,8, GAGE-3,4,5,6,7, GAS7,glypican-3, GnTV, gp100/Pmel17, GPNMB, HAUS3, Hepsin, HER-2/neu,HERV-K-MEL, HLA-A11, HLA-A2, HLA-DOB, hsp70-2, IDO1, IGF2B3,IL13Ralpha2, Intestinal carboxyl esterase, K-ras, Kallikrein 4, KIF20A,KK-LC-1, KKLC1, KM-HN-1, KMHN1 also known as CCDC110, LAGE-1,LDLR-fucosyltransferaseAS fusion protein, Lengsin, M-CSF, MAGE-A1,MAGE-A10, MAGE-A12, MAGE-A2, MAGE-A3, MAGE-A4, MAGE-A6, MAGE-A9,MAGE-C1, MAGE-C2, malic enzyme, mammaglobin-A, MART2, MATN, MC1R, MCSP,mdm-2, ME1, Melan-A/MART-1, Meloe, Midkine, MMP-2, MMP-7, MUC1, MUC5AC,mucin, MUM-1, MUM-2, MUM-3, Myosin, Myosin class I, N-raw, NA88-A,neo-PAP, NFYC, NY-BR-1, NY-ESO-1/LAGE-2, OA1, OGT, OS-9, P polypeptide,p53, PAP, PAX5, PBF, pml-RARalpha fusion protein, polymorphic epithelialmucin (“PEM”), PPP1R3B, PRAME, PRDX5, PSA, PSMA, PTPRK, RAB38/NY-MEL-1,RAGE-1, RBAF600, RGS5, RhoC, RNF43, RU2AS, SAGE, secernin 1, SIRT2,SNRPD1, SOX10, Sp17, SPA17, SSX-2, SSX-4, STEAP1, survivin, SYT-SSX1 or-SSX2 fusion protein, TAG-1, TAG-2, Telomerase, TGF-betaRII, TPBG,TRAG-3, Triosephosphate isomerase, TRP-1/gp75, TRP-2, TRP2-INT2,tyrosinase, tyrosinase (“TYR”), VEGF, WT1, XAGE-lb/GAGED2a. In someembodiments, the antigen is a neo-antigen.

In some embodiments, the cancer immunotherapy comprises administrationof a cancer-specific chimeric antigen receptor (CAR). In someembodiments, the CAR is administered on the surface of a T cell. In someembodiments, the CAR binds specifically to a cancer-associated antigen.

In some embodiments, the cancer immunotherapy comprises administrationof a cancer-specific T cell to the subject. In some embodiments, the Tcell is a CD4⁺ T cell. In some embodiments, the CD4⁺ T cell is a T_(H)1T cell, a T_(H)2 T cell or a T_(H)17 T cell. In some embodiments, the Tcell expresses a T cell receptor specific for a cancer-associatedantigen.

In some embodiments, the cancer vaccine is administered with anadjuvant. Examples of adjuvants include, but are not limited to, animmune modulatory protein, Adjuvant 65, α-GalCer, aluminum phosphate,aluminum hydroxide, calcium phosphate, β-Glucan Peptide, CpG DNA,GPI-0100, lipid A, lipopolysaccharide, Lipovant, Montanide,N-acetyl-muramyl-L-alanyl-D-isoglutamine, Pam3CSK4, quil A and trehalosedimycolate.

In some embodiments, the immunotherapy agent is an immune modulatingprotein to the subject. In some embodiments, the immune modulatoryprotein is a cytokine. Examples of immune modulating proteins include,but are not limited to, B lymphocyte chemoattractant (“BLC”), C-C motifchemokine 11 (“Eotaxin-1”), Eosinophil chemotactic protein 2(“Eotaxin-2”), Granulocyte colony-stimulating factor (“G-CSF”),Granulocyte macrophage colony-stimulating factor (“GM-CSF”), 1-309,Intercellular Adhesion Molecule 1 (“ICAM-1”), Interferon gamma(“IFN-gamma”), Interlukin-1 alpha (“IL-1 alpha”), Interlukin-1 beta(“IL-1 beta”), Interleukin 1 receptor antagonist (“IL-1 ra”),Interleukin-2 (“IL-2”), Interleukin-4 (“IL-4”), Interleukin-5 (“IL-5”),Interleukin-6 (“IL-6”), Interleukin-6 soluble receptor (“IL-6 sR”),Interleukin-7 (“IL-7”), Interleukin-8 (“IL-8”), Interleukin-10(“IL-10”), Interleukin-11 (“IL-11”), Subunit beta of Interleukin-12(“IL-12 p40” or “IL-12 p70”), Interleukin-13 (“IL-13”), Interleukin-15(“IL-15”), Interleukin-16 (“IL-16”), Interleukin-17 (“IL-17”), Chemokine(C-C motif) Ligand 2 (“MCP-1”), Macrophage colony-stimulating factor(“M-CSF”), Monokine induced by gamma interferon (“MIG”), Chemokine (C-Cmotif) ligand 2 (“MIP-1 alpha”), Chemokine (C-C motif) ligand 4 (“MIP-1beta”), Macrophage inflammatory protein-1-delta (“MIP-1 delta”),Platelet-derived growth factor subunit B (“PDGF-BB”), Chemokine (C-Cmotif) ligand 5, Regulated on Activation, Normal T cell Expressed andSecreted (“RANTES”), TIMP metallopeptidase inhibitor 1 (“TIMP-1”), TIMPmetallopeptidase inhibitor 2 (“TIMP-2”), Tumor necrosis factor,lymphotoxin-alpha (“TNF alpha”), Tumor necrosis factor, lymphotoxin-beta(“TNF beta”), Soluble TNF receptor type 1 (“sTNFRI”), sTNFRIIAR,Brain-derived neurotrophic factor (“BDNF”), Basic fibroblast growthfactor (“bFGF”), Bone morphogenetic protein 4 (“BMP-4”), Bonemorphogenetic protein 5 (“BMP-5”), Bone morphogenetic protein 7(“BMP-7”), Nerve growth factor (“b-NGF”), Epidermal growth factor(“EGF”), Epidermal growth factor receptor (“EGFR”),Endocrine-gland-derived vascular endothelial growth factor (“EG-VEGF”),Fibroblast growth factor 4 (“FGF-4”), Keratinocyte growth factor(“FGF-7”), Growth differentiation factor 15 (“GDF-15”), Glialcell-derived neurotrophic factor (“GDNF”), Growth Hormone,Heparin-binding EGF-like growth factor (“HB-EGF”), Hepatocyte growthfactor (“HGF”), Insulin-like growth factor binding protein 1(“IGFBP-1”), Insulin-like growth factor binding protein 2 (“IGFBP-2”),Insulin-like growth factor binding protein 3 (“IGFBP-3”), Insulin-likegrowth factor binding protein 4 (“IGFBP-4”), Insulin-like growth factorbinding protein 6 (“IGFBP-6”), Insulin-like growth factor 1 (“IGF-1”),Insulin, Macrophage colony-stimulating factor (“M-CSF R”), Nerve growthfactor receptor (“NGF R”), Neurotrophin-3 (“NT-3”), Neurotrophin-4(“NT-4”), Osteoclastogenesis inhibitory factor (“Osteoprotegerin”),Platelet-derived growth factor receptors (“PDGF-AA”),Phosphatidylinositol-glycan biosynthesis (“PIGF”), Skp, Cullin, F-boxcontaining comples (“SCF”), Stem cell factor receptor (“SCF R”),Transforming growth factor alpha (“TGFalpha”), Transforming growthfactor beta-1 (“TGF beta 1”), Transforming growth factor beta-3 (“TGFbeta 3”), Vascular endothelial growth factor (“VEGF”), Vascularendothelial growth factor receptor 2 (“VEGFR2”), Vascular endothelialgrowth factor receptor 3 (“VEGFR3”), VEGF-D 6Ckine, Tyrosine-proteinkinase receptor UFO (“Axl”), Betacellulin (“BTC”), Mucosae-associatedepithelial chemokine (“CCL28”), Chemokine (C-C motif) ligand 27(“CTACK”), Chemokine (C-X-C motif) ligand 16 (“CXCL16”), C-X-C motifchemokine 5 (“ENA-78”), Chemokine (C-C motif) ligand 26 (“Eotaxin-3”),Granulocyte chemotactic protein 2 (“GCP-2”), GRO, Chemokine (C-C motif)ligand 14 (“HCC-1”), Chemokine (C-C motif) ligand 16 (“HCC-4”),Interleukin-9 (“IL-9”), Interleukin-17 F (“IL-17F”),Interleukin-18-binding protein (“IL-18 BPa”), Interleukin-28 A(“IL-28A”), Interleukin 29 (“IL-29”), Interleukin 31 (“IL-31”), C-X-Cmotif chemokine 10 (“IP-10”), Chemokine receptor CXCR3 (“I-TAC”),Leukemia inhibitory factor (“LIF”), Light, Chemokine (C motif) ligand(“Lymphotactin”), Monocyte chemoattractant protein 2 (“MCP-2”), Monocytechemoattractant protein 3 (“MCP-3”), Monocyte chemoattractant protein 4(“MCP-4”), Macrophage-derived chemokine (“MDC”), Macrophage migrationinhibitory factor (“MIF”), Chemokine (C-C motif) ligand 20 (“MIP-3alpha”), C-C motif chemokine 19 (“MIP-3 beta”), Chemokine (C-C motif)ligand 23 (“MPIF-1”), Macrophage stimulating protein alpha chain(“MSPalpha”), Nucleosome assembly protein 1-like 4 (“NAP-2”), Secretedphosphoprotein 1 (“Osteopontin”), Pulmonary and activation-regulatedcytokine (“PARC”), Platelet factor 4 (“PF4”), Stroma cell-derivedfactor-1 alpha (“SDF-1 alpha”), Chemokine (C-C motif) ligand 17(“TARC”), Thymus-expressed chemokine (“TECK”), Thymic stromallymphopoietin (“TSLP 4-IBB”), CD 166 antigen (“ALCAM”), Cluster ofDifferentiation 80 (“B7-1”), Tumor necrosis factor receptor superfamilymember 17 (“BCMA”), Cluster of Differentiation 14 (“CD14”), Cluster ofDifferentiation 30 (“CD30”), Cluster of Differentiation 40 (“CD40Ligand”), Carcinoembryonic antigen-related cell adhesion molecule 1(biliary glycoprotein) (“CEACAM-1”), Death Receptor 6 (“DR6”),Deoxythymidine kinase (“Dtk”), Type 1 membrane glycoprotein(“Endoglin”), Receptor tyrosine-protein kinase erbB-3 (“ErbB3”),Endothelial-leukocyte adhesion molecule 1 (“E-Selectin”), Apoptosisantigen 1 (“Fas”), Fms-like tyrosine kinase 3 (“Flt-3L”), Tumor necrosisfactor receptor superfamily member 1 (“GITR”), Tumor necrosis factorreceptor superfamily member 14 (“HVEM”), Intercellular adhesion molecule3 (“ICAM-3”), IL-1 R4, IL-1 RI, IL-10 Rbeta, IL-17R, IL-2Rgamma, IL-21R,Lysosome membrane protein 2 (“LIMPII”), Neutrophil gelatinase-associatedlipocalin (“Lipocalin-2”), CD62L (“L-Selectin”), Lymphatic endothelium(“LYVE-1”), MHC class I polypeptide-related sequence A (“MICA”), MHCclass I polypeptide-related sequence B (“MICB”), NRG1-betal, Beta-typeplatelet-derived growth factor receptor (“PDGF Rbeta”), Plateletendothelial cell adhesion molecule (“PECAM-1”), RAGE, Hepatitis A viruscellular receptor 1 (“TIM-1”), Tumor necrosis factor receptorsuperfamily member IOC (“TRAIL R3”), Trappin protein transglutaminasebinding domain (“Trappin-2”), Urokinase receptor (“uPAR”), Vascular celladhesion protein 1 (“VCAM-1”), XEDARActivin A, Agouti-related protein(“AgRP”), Ribonuclease 5 (“Angiogenin”), Angiopoietin 1, Angiostatin,Catheprin S, CD40, Cryptic family protein IB (“Cripto-1”), DAN,Dickkopf-related protein 1 (“DKK-1”), E-Cadherin, Epithelial celladhesion molecule (“EpCAM”), Fas Ligand (FasL or CD95L), Fcg RIIB/C,FoUistatin, Galectin-7, Intercellular adhesion molecule 2 (“ICAM-2”),IL-13 R1, IL-13R2, IL-17B, IL-2 Ra, IL-2 Rb, IL-23, LAP, Neuronal celladhesion molecule (“NrCAM”), Plasminogen activator inhibitor-1(“PAI-1”), Platelet derived growth factor receptors (“PDGF-AB”),Resistin, stromal cell-derived factor 1 (“SDF-1 beta”), sgp130, Secretedfrizzled-related protein 2 (“ShhN”), Sialic acid-bindingimmunoglobulin-type lectins (“Siglec-5”), ST2, Transforming growthfactor-beta 2 (“TGF beta 2”), Tie-2, Thrombopoietin (“TPO”), Tumornecrosis factor receptor superfamily member 10D (“TRAIL R4”), Triggeringreceptor expressed on myeloid cells 1 (“TREM-1”), Vascular endothelialgrowth factor C (“VEGF-C”), VEGFR1Adiponectin, Adipsin (“AND”),Alpha-fetoprotein (“AFP”), Angiopoietin-like 4 (“ANGPTL4”),Beta-2-microglobulin (“B2M”), Basal cell adhesion molecule (“BCAM”),Carbohydrate antigen 125 (“CA125”), Cancer Antigen 15-3 (“CA15-3”),Carcinoembryonic antigen (“CEA”), cAMP receptor protein (“CRP”), HumanEpidermal Growth Factor Receptor 2 (“ErbB2”), Follistatin,Follicle-stimulating hormone (“FSH”), Chemokine (C-X-C motif) ligand 1(“GRO alpha”), human chorionic gonadotropin (“beta HCG”), Insulin-likegrowth factor 1 receptor (“IGF-1 sR”), IL-1 sRII, IL-3, IL-18 Rb, IL-21,Leptin, Matrix metalloproteinase-1 (“MMP-1”), Matrix metalloproteinase-2(“MMP-2”), Matrix metalloproteinase-3 (“MMP-3”), Matrixmetalloproteinase-8 (“MMP-8”), Matrix metalloproteinase-9 (“MMP-9”),Matrix metalloproteinase-10 (“MMP-10”), Matrix metalloproteinase-13(“MMP-13”), Neural Cell Adhesion Molecule (“NCAM-1”), Entactin(“Nidogen-1”), Neuron specific enolase (“NSE”), Oncostatin M (“OSM”),Procalcitonin, Prolactin, Prostate specific antigen (“PSA”), Sialicacid-binding Ig-like lectin 9 (“Siglec-9”), ADAM 17 endopeptidase(“TACE”), Thyroglobulin, Metalloproteinase inhibitor 4 (“TIMP-4”),TSH2B4, Disintegrin and metalloproteinase domain-containing protein 9(“ADAM-9”), Angiopoietin 2, Tumor necrosis factor ligand superfamilymember 13/Acidic leucine-rich nuclear phosphoprotein 32 family member B(“APRIL”), Bone morphogenetic protein 2 (“BMP-2”), Bone morphogeneticprotein 9 (“BMP-9”), Complement component 5a (“C5a”), Cathepsin L,CD200, CD97, Chemerin, Tumor necrosis factor receptor superfamily member6B (“DcR3”), Fatty acid-binding protein 2 (“FABP2”), Fibroblastactivation protein, alpha (“FAP”), Fibroblast growth factor 19(“FGF-19”), Galectin-3, Hepatocyte growth factor receptor (“HGF R”),IFN-gammalpha/beta R2, Insulin-like growth factor 2 (“IGF-2”),Insulin-like growth factor 2 receptor (“IGF-2 R”), Interleukin-1receptor 6 (“IL-1R6”), Interleukin 24 (“IL-24”), Interleukin 33(“IL-33”, Kallikrein 14, Asparaginyl endopeptidase (“Legumain”),Oxidized low-density lipoprotein receptor 1 (“LOX-1”), Mannose-bindinglectin (“MBL”), Neprilysin (“NEP”), Notch homolog 1,translocation-associated (Drosophila) (“Notch-1”), Nephroblastomaoverexpressed (“NOV”), Osteoactivin, Programmed cell death protein 1(“PD-1”), N-acetylmuramoyl-L-alanine amidase (“PGRP-5”), Serpin A4,Secreted frizzled related protein 3 (“sFRP-3”), Thrombomodulin, Tolllikereceptor 2 (“TLR2”), Tumor necrosis factor receptor superfamily member10A (“TRAIL R1”), Transferrin (“TRF”), WIF-1ACE-2, Albumin, AMICA,Angiopoietin 4, B-cell activating factor (“BAFF”), Carbohydrate antigen19-9 (“CA19-9”), CD 163, Clusterin, CRT AM, Chemokine (C-X-C motif)ligand 14 (“CXCL14”), Cystatin C, Decorin (“DCN”), Dickkopf-relatedprotein 3 (“Dkk-3”), Delta-like protein 1 (“DLL1”), Fetuin A,Heparin-binding growth factor 1 (“aFGF”), Folate receptor alpha(“FOLR1”), Furin, GPCR-associated sorting protein 1 (“GASP-1”),GPCR-associated sorting protein 2 (“GASP-2”), Granulocytecolony-stimulating factor receptor (“GCSF R”), Serine protease hepsin(“HAI-2”), Interleukin-17B Receptor (“IL-17B R”), Interleukin 27(“IL-27”), Lymphocyte-activation gene 3 (“LAG-3”), Apolipoprotein A-V(“LDL R”), Pepsinogen I, Retinol binding protein 4 (“RBP4”), SOST,Heparan sulfate proteoglycan (“Syndecan-1”), Tumor necrosis factorreceptor superfamily member 13B (“TACI”), Tissue factor pathwayinhibitor (“TFPI”), TSP-1, Tumor necrosis factor receptor superfamily,member 10b (“TRAIL R2”), TRANCE, Troponin I, Urokinase PlasminogenActivator (“uPA”), Cadherin 5, type 2 or VE-cadherin (vascularendothelial) also known as CD144 (“VE-Cadherin”),WNT1-inducible-signaling pathway protein 1 (“WISP-1”), and ReceptorActivator of Nuclear Factor κB (“RANK”).

In some embodiments, the cancer therapeutic is a radioactive moiety thatcomprises a radionuclide. Exemplary radionuclides include, but are notlimited to Cr-51, Cs-131, Ce-134, Se-75, Ru-97, I-125, Eu-149, Os-189m,Sb-119, I-123, Ho-161, Sb-117, Ce-139, In-111, Rh-103m, Ga-67, Tl-201,Pd-103, Au-195, Hg-197, Sr-87m, Pt-191, P-33, Er-169, Ru-103, Yb-169,Au-199, Sn-121, Tm-167, Yb-175, In-113m, Sn-113, Lu-177, Rh-105,Sn-117m, Cu-67, Sc-47, Pt-195m, Ce-141, I-131, Tb-161, As-77, Pt-197,Sm-153, Gd-159, Tm-173, Pr-143, Au-198, Tm-170, Re-186, Ag-111, Pd-109,Ga-73, Dy-165, Pm-149, Sn-123, Sr-89, Ho-166, P-32, Re-188, Pr-142,Ir-194, In-114m/In-114, and Y-90.

In some embodiments, the cancer therapeutic is an angiogenesis inhibitorto the subject. Examples of such angiogenesis inhibitors include, butare not limited to Bevacizumab (Avastin®), Ziv-aflibercept (Zaltrap®),Sorafenib (Nexavar®), Sunitinib (Sutent®), Pazopanib (Votrient®),Regorafenib (Stivarga®), and Cabozantinib (Cometrig™).

In some embodiments, the cancer therapeutic is an antibiotic. Forexample, if the presence of a cancer-associated bacteria and/or acancer-associated microbiome profile is detected according to themethods provided herein, antibiotics can be administered to eliminatethe cancer-associated bacteria from the subject. “Antibiotics” broadlyrefers to compounds capable of inhibiting or preventing a bacterialinfection. Antibiotics can be classified in a number of ways, includingtheir use for specific infections, their mechanism of action, theirbioavailability, or their spectrum of target microbe (e.g.,Gram-negative vs. Gram-positive bacteria, aerobic vs. anaerobicbacteria, etc.) and these may be used to kill specific bacteria inspecific areas of the host (“niches”) (Leekha, et al 2011. GeneralPrinciples of Antimicrobial Therapy. Mayo Clin Proc. 86(2): 156-167). Incertain embodiments, antibiotics can be used to selectively targetbacteria of a specific niche. In some embodiments, antibiotics known totreat a particular infection that includes a cancer niche may be used totarget cancer-associated microbes, including cancer-associated bacteriain that niche. In other embodiments, antibiotics are administered afterthe bacterial treatment. In some embodiments, antibiotics areadministered after the bacterial treatment to remove the engraftment.

In some aspects, antibiotics can be selected based on their bactericidalor bacteriostatic properties. Bactericidal antibiotics includemechanisms of action that disrupt the cell wall (e.g., β-lactams), thecell membrane (e.g., daptomycin), or bacterial DNA (e.g.,fluoroquinolones). Bacteriostatic agents inhibit bacterial replicationand include sulfonamides, tetracyclines, and macrolides, and act byinhibiting protein synthesis. Furthermore, while some drugs can bebactericidal in certain organisms and bacteriostatic in others, knowingthe target organism allows one skilled in the art to select anantibiotic with the appropriate properties. In certain treatmentconditions, bacteriostatic antibiotics inhibit the activity ofbactericidal antibiotics. Thus, in certain embodiments, bactericidal andbacteriostatic antibiotics are not combined.

Antibiotics include, but are not limited to aminoglycosides, ansamycins,carbacephems, carbapenems, cephalosporins, glycopeptides, lincosamides,lipopeptides, macrolides, monobactams, nitrofurans, oxazolidonones,penicillins, polypeptide antibiotics, quinolones, fluoroquinolone,sulfonamides, tetracyclines, and anti-mycobacterial compounds, andcombinations thereof.

Aminoglycosides include, but are not limited to Amikacin, Gentamicin,Kanamycin, Neomycin, Netilmicin, Tobramycin, Paromomycin, andSpectinomycin. Aminoglycosides are effective, e.g., againstGram-negative bacteria, such as Escherichia coli, Klebsiella,Pseudomonas aeruginosa, and Francisella tularensis, and against certainaerobic bacteria but less effective against obligate/facultativeanaerobes. Aminoglycosides are believed to bind to the bacterial 30S or50S ribosomal subunit thereby inhibiting bacterial protein synthesis.

Ansamycins include, but are not limited to, Geldanamycin, Herbimycin,Rifamycin, and Streptovaricin. Geldanamycin and Herbimycin are believedto inhibit or alter the function of Heat Shock Protein 90.

Carbacephems include, but are not limited to, Loracarbef. Carbacephemsare believed to inhibit bacterial cell wall synthesis.

Carbapenems include, but are not limited to, Ertapenem, Doripenem,Imipenem/Cilastatin, and Meropenem. Carbapenems are bactericidal forboth Gram-positive and Gram-negative bacteria as broad-spectrumantibiotics. Carbapenems are believed to inhibit bacterial cell wallsynthesis.

Cephalosporins include, but are not limited to, Cefadroxil, Cefazolin,Cefalotin, Cefalothin, Cefalexin, Cefaclor, Cefamandole, Cefoxitin,Cefprozil, Cefuroxime, Cefixime, Cefdinir, Cefditoren, Cefoperazone,Cefotaxime, Cefpodoxime, Ceftazidime, Ceftibuten, Ceftizoxime,Ceftriaxone, Cefepime, Ceftaroline fosamil,and Ceftobiprole. SelectedCephalosporins are effective, e.g., against Gram-negative bacteria andagainst Gram-positive bacteria, including Pseudomonas, certainCephalosporins are effective against methicillin-resistantStaphylococcus aureus (MRSA). Cephalosporins are believed to inhibitbacterial cell wall synthesis by disrupting synthesis of thepeptidoglycan layer of bacterial cell walls.

Glycopeptides include, but are not limited to, Teicoplanin, Vancomycin,and Telavancin. Glycopeptides are effective, e.g., against aerobic andanaerobic Gram-positive bacteria including MRSA and Clostridiumdifficile. Glycopeptides are believed to inhibit bacterial cell wallsynthesis by disrupting synthesis of the peptidoglycan layer ofbacterial cell walls.

Lincosamides include, but are not limited to, Clindamycin andLincomycin. Lincosamides are effective, e.g., against anaerobicbacteria, as well as Staphylococcus, and Streptococcus. Lincosamides arebelieved to bind to the bacterial 50S ribosomal subunit therebyinhibiting bacterial protein synthesis.

Lipopeptides include, but are not limited to, Daptomycin. Lipopeptidesare effective, e.g., against Gram-positive bacteria. Lipopeptides arebelieved to bind to the bacterial membrane and cause rapiddepolarization.

Macrolides include, but are not limited to, Azithromycin,Clarithromycin, Dirithromycin, Erythromycin, Roxithromycin,Troleandomycin, Telithromycin, and Spiramycin. Macrolides are effective,e.g., against Streptococcus and Mycoplasma. Macrolides are believed tobind to the bacterial or 50S ribosomal subunit, thereby inhibitingbacterial protein synthesis.

Monobactams include, but are not limited to, Aztreonam. Monobactams areeffective, e.g., against Gram-negative bacteria. Monobactams arebelieved to inhibit bacterial cell wall synthesis by disruptingsynthesis of the peptidoglycan layer of bacterial cell walls.

Nitrofurans include, but are not limited to, Furazolidone andNitrofurantoin.

Oxazolidonones include, but are not limited to, Linezolid, Posizolid,Radezolid, and Torezolid. Oxazolidonones are believed to be proteinsynthesis inhibitors.

Penicillins include, but are not limited to, Amoxicillin, Ampicillin,Azlocillin, Carbenicillin, Cloxacillin, Dicloxacillin, Flucloxacillin,Mezlocillin, Methicillin, Nafcillin, Oxacillin, Penicillin G, PenicillinV, Piperacillin, Temocillin and Ticarcillin. Penicillins are effective,e.g., against Gram-positive bacteria, facultative anaerobes, e.g.,Streptococcus, Borrelia, and Treponema. Penicillins are believed toinhibit bacterial cell wall synthesis by disrupting synthesis of thepeptidoglycan layer of bacterial cell walls.

Penicillin combinations include, but are not limited to,Amoxicillin/clavulanate, Ampicillin/sulbactam, Piperacillin/tazobactam,and Ticarcillin/clavulanate.

Polypeptide antibiotics include, but are not limited to, Bacitracin,Colistin, and Polymyxin B and E. Polypeptide Antibiotics are effective,e.g., against Gram-negative bacteria. Certain polypeptide antibioticsare believed to inhibit isoprenyl pyrophosphate involved in synthesis ofthe peptidoglycan layer of bacterial cell walls, while othersdestabilize the bacterial outer membrane by displacing bacterialcounter-ions.

Quinolones and Fluoroquinolone include, but are not limited to,Ciprofloxacin, Enoxacin, Gatifloxacin, Gemifloxacin, Levofloxacin,Lomefloxacin, Moxifloxacin, Nalidixic acid, Norfloxacin, Ofloxacin,Trovafloxacin, Grepafloxacin, Sparfloxacin, and Temafloxacin.Quinolones/Fluoroquinolone are effective, e.g., against Streptococcusand Neisseria. Quinolones/Fluoroquinolone are believed to inhibit thebacterial DNA gyrase or topoisomerase IV, thereby inhibiting DNAreplication and transcription.

Sulfonamides include, but are not limited to, Mafenide, Sulfacetamide,Sulfadiazine, Silver sulfadiazine, Sulfadimethoxine, Sulfamethizole,Sulfamethoxazole, Sulfanilimide, Sulfasalazine, Sulfisoxazole,Trimethoprim-Sulfamethoxazole (Co-trimoxazole), andSulfonamidochrysoidine. Sulfonamides are believed to inhibit folatesynthesis by competitive inhibition of dihydropteroate synthetase,thereby inhibiting nucleic acid synthesis.

Tetracyclines include, but are not limited to, Demeclocycline,Doxycycline, Minocycline, Oxytetracycline, and Tetracycline.Tetracyclines are effective, e.g., against Gram-negative bacteria.Tetracyclines are believed to bind to the bacterial 30S ribosomalsubunit thereby inhibiting bacterial protein synthesis.

Anti-mycobacterial compounds include, but are not limited to,Clofazimine, Dapsone, Capreomycin, Cycloserine, Ethambutol, Ethionamide,Isoniazid, Pyrazinamide, Rifampicin, Rifabutin, Rifapentine, andStreptomycin.

Suitable antibiotics also include arsphenamine, chloramphenicol,fosfomycin, fusidic acid, metronidazole, mupirocin, platensimycin,quinupristin/dalfopristin, tigecycline, tinidazole, trimethoprimamoxicillin/clavulanate, ampicillin/sulbactam, amphomycin ristocetin,azithromycin, bacitracin, buforin II, carbomycin, cecropin Pl,clarithromycin, erythromycins, furazolidone, fusidic acid, Na fusidate,gramicidin, imipenem, indolicidin, josamycin, magainan II,metronidazole, nitroimidazoles, mikamycin, mutacin B-Ny266, mutacinB-JHl 140, mutacin J-T8, nisin, nisin A, novobiocin, oleandomycin,ostreogrycin, piperacillin/tazobactam, pristinamycin, ramoplanin,ranalexin, reuterin, rifaximin, rosamicin, rosaramicin, spectinomycin,spiramycin, staphylomycin, streptogramin, streptogramin A, synergistin,taurolidine, teicoplanin, telithromycin, ticarcillin/clavulanic acid,triacetyloleandomycin, tylosin, tyrocidin, tyrothricin, vancomycin,vemamycin, and virginiamycin.

In some embodiments, the the cancer therapy comprises administering atherapeutic bacteria and/or a therapeutic combination of bacteria to thesubject so a healthy microbiome can be reconstituted in the subject. Insome embodiments, the therapeutic bacteria is a non-cancer-associatedbacteria. In some embodiments the therapeutic bacteria is a probioticbacteria.

Cancer

In some embodiments, the methods and compositions described hereinrelate to the treatment of cancer. Examples of cancers that may treatedby methods described herein include, but are not limited to,hematological malignancy, acute nonlymphocytic leukemia, chroniclymphocytic leukemia, acute granulocytic leukemia, chronic granulocyticleukemia, acute promyelocytic leukemia, adult T-cell leukemia, aleukemicleukemia, a leukocythemic leukemia, basophilic leukemia, blast cellleukemia, bovine leukemia, chronic myelocytic leukemia, leukemia cutis,embryonal leukemia, eosinophilic leukemia, Gross' leukemia, Rieder cellleukemia, Schilling's leukemia, stem cell leukemia, subleukemicleukemia, undifferentiated cell leukemia, hairy-cell leukemia,hemoblastic leukemia, hemocytoblastic leukemia, histiocytic leukemia,stem cell leukemia, acute monocytic leukemia, leukopenic leukemia,lymphatic leukemia, lymphoblastic leukemia, lymphocytic leukemia,lymphogenous leukemia, lymphoid leukemia, lymphosarcoma cell leukemia,mast cell leukemia, megakaryocytic leukemia, micromyeloblastic leukemia,monocytic leukemia, myeloblastic leukemia, myelocytic leukemia, myeloidgranulocytic leukemia, myelomonocytic leukemia, Naegeli leukemia, plasmacell leukemia, plasmacytic leukemia, promyelocytic leukemia, acinarcarcinoma, acinous carcinoma, adenocystic carcinoma, adenoid cysticcarcinoma, carcinoma adenomatosum, carcinoma of adrenal cortex, alveolarcarcinoma, alveolar cell carcinoma, basal cell carcinoma, carcinomabasocellulare, basaloid carcinoma, basosquamous cell carcinoma,bronchioalveolar carcinoma, bronchiolar carcinoma, bronchogeniccarcinoma, cerebriform carcinoma, cholangiocellular carcinoma, chorioniccarcinoma, colloid carcinoma, comedo carcinoma, corpus carcinoma,cribriform carcinoma, carcinoma en cuirasse, carcinoma cutaneum,cylindrical carcinoma, cylindrical cell carcinoma, duct carcinoma,carcinoma durum, embryonal carcinoma, encephaloid carcinoma, epiennoidcarcinoma, carcinoma epitheliale adenoides, exophytic carcinoma,carcinoma ex ulcere, carcinoma fibrosum, gelatiniform carcinoma,gelatinous carcinoma, giant cell carcinoma, signet-ring cell carcinoma,carcinoma simplex, small-cell carcinoma, solanoid carcinoma, spheroidalcell carcinoma, spindle cell carcinoma, carcinoma spongiosum, squamouscarcinoma, squamous cell carcinoma, string carcinoma, carcinomatelangiectaticum, carcinoma telangiectodes, transitional cell carcinoma,carcinoma tuberosum, tuberous carcinoma, verrucous carcinoma, carcinomavillosum, carcinoma gigantocellulare, glandular carcinoma, granulosacell carcinoma, hair-matrix carcinoma, hematoid carcinoma,hepatocellular carcinoma, Hurthle cell carcinoma, hyaline carcinoma,hypernephroid carcinoma, infantile embryonal carcinoma, carcinoma insitu, intraepidermal carcinoma, intraepithelial carcinoma, Krompecher'scarcinoma, Kulchitzky-cell carcinoma, large-cell carcinoma, lenticularcarcinoma, carcinoma lenticulare, lipomatous carcinoma, lymphoepithelialcarcinoma, carcinoma medullare, medullary carcinoma, melanoticcarcinoma, carcinoma molle, mucinous carcinoma, carcinoma muciparum,carcinoma mucocellulare, mucoepidermoid carcinoma, carcinoma mucosum,mucous carcinoma, carcinoma myxomatodes, naspharyngeal carcinoma, oatcell carcinoma, carcinoma ossificans, osteoid carcinoma, papillarycarcinoma, periportal carcinoma, preinvasive carcinoma, prickle cellcarcinoma, pultaceous carcinoma, renal cell carcinoma of kidney, reservecell carcinoma, carcinoma sarcomatodes, schneiderian carcinoma,scirrhous carcinoma, carcinoma scroti, chondrosarcoma, fibrosarcoma,lymphosarcoma, melanosarcoma, myxosarcoma, osteosarcoma, endometrialsarcoma, stromal sarcoma, Ewing' s sarcoma, fascial sarcoma,fibroblastic sarcoma, giant cell sarcoma, Abemethy's sarcoma, adiposesarcoma, liposarcoma, alveolar soft part sarcoma, ameloblastic sarcoma,botryoid sarcoma, chloroma sarcoma, chorio carcinoma, embryonal sarcoma,Wilms' tumor sarcoma, granulocytic sarcoma, Hodgkin's sarcoma,idiopathic multiple pigmented hemorrhagic sarcoma, immunoblastic sarcomaof B cells, lymphoma, immunoblastic sarcoma of T-cells, Jensen'ssarcoma, Kaposi's sarcoma, Kupffer cell sarcoma, angiosarcoma,leukosarcoma, malignant mesenchymoma sarcoma, parosteal sarcoma,reticulocytic sarcoma, rhabdosarcoma, serocystic sarcoma, synovialsarcoma, telangiectaltic sarcoma, Hodgkin's Disease, Non-Hodgkin'sLymphoma, multiple myeloma, neuroblastoma, bladder cancer, breastcancer, ovarian cancer, lung cancer, colorectal cancer,rhabdomyosarcoma, primary thrombocytosis, primary macroglobulinemia,small-cell lung tumors, primary brain tumors, stomach cancer, coloncancer, malignant pancreatic insulanoma, malignant carcinoid,premalignant skin lesions, testicular cancer, lymphomas, thyroid cancer,neuroblastoma, esophageal cancer, genitourinary tract cancer, malignanthypercalcemia, cervical cancer, endometrial cancer, adrenal corticalcancer, Harding-Passey melanoma, juvenile melanoma, lentigo malignamelanoma, malignant melanoma, acral-lentiginous melanoma, amelanoticmelanoma, benign juvenile melanoma, Cloudman's melanoma, S91 melanoma,nodular melanoma subungal melanoma, and superficial spreading melanoma.

In some embodiments, the methods and compositions provided herein relateto the treatment of a leukemia. The term “leukemia” is meant broadlyprogressive, malignant diseases of the hematopoietic organs/systems andis generally characterized by a distorted proliferation and developmentof leukocytes and their precursors in the blood and bone marrow.Non-limiting examples of leukemia diseases include, acute nonlymphocyticleukemia, chronic lymphocytic leukemia, acute granulocytic leukemia,chronic granulocytic leukemia, acute promyelocytic leukemia, adultT-cell leukemia, aleukemic leukemia, a leukocythemic leukemia,basophilic leukemia, blast cell leukemia, bovine leukemia, chronicmyelocytic leukemia, leukemia cutis, embryonal leukemia, eosinophilicleukemia, Gross' leukemia, Rieder cell leukemia, Schilling's leukemia,stem cell leukemia, subleukemic leukemia, undifferentiated cellleukemia, hairy-cell leukemia, hemoblastic leukemia, hemocytoblasticleukemia, histiocytic leukemia, stem cell leukemia, acute monocyticleukemia, leukopenic leukemia, lymphatic leukemia, lymphoblasticleukemia, lymphocytic leukemia, lymphogenous leukemia, lymphoidleukemia, lymphosarcoma cell leukemia, mast cell leukemia,megakaryocytic leukemia, micromyeloblastic leukemia, monocytic leukemia,myeloblastic leukemia, myelocytic leukemia, myeloid granulocyticleukemia, myelomonocytic leukemia, Naegeli leukemia, plasma cellleukemia, plasmacytic leukemia, and promyelocytic leukemia.

In some embodiments, the methods and compositions provided herein relateto the treatment of a carcinoma. The term “carcinoma” refers to amalignant growth made up of epithelial cells tending to infiltrate thesurrounding tissues, and/or resist physiological and non-physiologicalcell death signals and gives rise to metastases. Non-limiting exemplarytypes of carcinomas include, acinar carcinoma, acinous carcinoma,adenocystic carcinoma, adenoid cystic carcinoma, carcinoma adenomatosum,carcinoma of adrenal cortex, alveolar carcinoma, alveolar cellcarcinoma, basal cell carcinoma, carcinoma basocellulare, basaloidcarcinoma, basosquamous cell carcinoma, bronchioalveolar carcinoma,bronchiolar carcinoma, bronchogenic carcinoma, cerebriform carcinoma,cholangiocellular carcinoma, chorionic carcinoma, colloid carcinoma,comedo carcinoma, corpus carcinoma, cribriform carcinoma, carcinoma encuirasse, carcinoma cutaneum, cylindrical carcinoma, cylindrical cellcarcinoma, duct carcinoma, carcinoma durum, embryonal carcinoma,encephaloid carcinoma, epiennoid carcinoma, carcinoma epithelialeadenoides, exophytic carcinoma, carcinoma ex ulcere, carcinoma fibrosum,gelatiniform carcinoma, gelatinous carcinoma, giant cell carcinoma,signet-ring cell carcinoma, carcinoma simplex, small-cell carcinoma,solanoid carcinoma, spheroidal cell carcinoma, spindle cell carcinoma,carcinoma spongiosum, squamous carcinoma, squamous cell carcinoma,string carcinoma, carcinoma telangiectaticum, carcinoma telangiectodes,transitional cell carcinoma, carcinoma tuberosum, tuberous carcinoma,verrucous carcinoma, carcinoma villosum, carcinoma gigantocellulare,glandular carcinoma, granulosa cell carcinoma, hair-matrix carcinoma,hematoid carcinoma, hepatocellular carcinoma, Hurthle cell carcinoma,hyaline carcinoma, hypernephroid carcinoma, infantile embryonalcarcinoma, carcinoma in situ, intraepidermal carcinoma, intraepithelialcarcinoma, Krompecher's carcinoma, Kulchitzky-cell carcinoma, large-cellcarcinoma, lenticular carcinoma, carcinoma lenticulare, lipomatouscarcinoma, lymphoepithelial carcinoma, carcinoma medullare, medullarycarcinoma, melanotic carcinoma, carcinoma molle, mucinous carcinoma,carcinoma muciparum, carcinoma mucocellulare, mucoepidermoid carcinoma,carcinoma mucosum, mucous carcinoma, carcinoma myxomatodes,naspharyngeal carcinoma, oat cell carcinoma, carcinoma ossificans,osteoid carcinoma, papillary carcinoma, periportal carcinoma,preinvasive carcinoma, prickle cell carcinoma, pultaceous carcinoma,renal cell carcinoma of kidney, reserve cell carcinoma, carcinomasarcomatodes, schneiderian carcinoma, scirrhous carcinoma, and carcinomascroti.

In some embodiments, the methods and compositions provided herein relateto the treatment of a sarcoma. The term “sarcoma” generally refers to atumor which is made up of a substance like the embryonic connectivetissue and is generally composed of closely packed cells embedded in afibrillar, heterogeneous, or homogeneous substance. Sarcomas include,but are not limited to, chondrosarcoma, fibrosarcoma, lymphosarcoma,melanosarcoma, myxosarcoma, osteosarcoma, endometrial sarcoma, stromalsarcoma, Ewing' s sarcoma, fascial sarcoma, fibroblastic sarcoma, giantcell sarcoma, Abemethy's sarcoma, adipose sarcoma, liposarcoma, alveolarsoft part sarcoma, ameloblastic sarcoma, botryoid sarcoma, chloromasarcoma, chorio carcinoma, embryonal sarcoma, Wilms' tumor sarcoma,granulocytic sarcoma, Hodgkin's sarcoma, idiopathic multiple pigmentedhemorrhagic sarcoma, immunoblastic sarcoma of B cells, lymphoma,immunoblastic sarcoma of T-cells, Jensen's sarcoma, Kaposi's sarcoma,Kupffer cell sarcoma, angiosarcoma, leukosarcoma, malignant mesenchymomasarcoma, parosteal sarcoma, reticulocytic sarcoma, Rous sarcoma,serocystic sarcoma, synovial sarcoma, and telangiectaltic sarcoma.

Additional exemplary neoplasias that can be treated using the methodsand compositions described herein include Hodgkin's Disease,Non-Hodgkin's Lymphoma, multiple myeloma, neuroblastoma, breast cancer,ovarian cancer, lung cancer, rhabdomyosarcoma, primary thrombocytosis,primary macroglobulinemia, small-cell lung tumors, primary brain tumors,stomach cancer, colon cancer, malignant pancreatic insulanoma, malignantcarcinoid, premalignant skin lesions, testicular cancer, lymphomas,thyroid cancer, neuroblastoma, esophageal cancer, genitourinary tractcancer, malignant hypercalcemia, cervical cancer, endometrial cancer,and adrenal cortical cancer.

In some embodiments, the cancer treated is a melanoma. The term“melanoma” is taken to mean a tumor arising from the melanocytic systemof the skin and other organs. Non-limiting examples of melanomas areHarding-Passey melanoma, juvenile melanoma, lentigo maligna melanoma,malignant melanoma, acral-lentiginous melanoma, amelanotic melanoma,benign juvenile melanoma, Cloudman's melanoma, S91 melanoma, nodularmelanoma subungal melanoma, and superficial spreading melanoma.

Particular categories of tumors that can be treated using methods andcompositions described herein include lymphoproliferative disorders,breast cancer, ovarian cancer, prostate cancer, cervical cancer,endometrial cancer, bone cancer, liver cancer, stomach cancer, coloncancer, colorectal cancer, pancreatic cancer, cancer of the thyroid,head and neck cancer, cancer of the central nervous system, cancer ofthe peripheral nervous system, skin cancer, kidney cancer, as well asmetastases of all the above. Particular types of tumors includehepatocellular carcinoma, hepatoma, hepatoblastoma, rhabdomyosarcoma,esophageal carcinoma, thyroid carcinoma, ganglioblastoma, fibrosarcoma,myxosarcoma, liposarcoma, chondrosarcoma, osteogenic sarcoma, chordoma,angiosarcoma, endotheliosarcoma, Ewing's tumor, leimyosarcoma,rhabdotheliosarcoma, invasive ductal carcinoma, papillaryadenocarcinoma, melanoma, pulmonary squamous cell carcinoma, basal cellcarcinoma, adenocarcinoma (well differentiated, moderatelydifferentiated, poorly differentiated or undifferentiated),bronchioloalveolar carcinoma, renal cell carcinoma, hypernephroma,hypernephroid adenocarcinoma, bile duct carcinoma, choriocarcinoma,seminoma, embryonal carcinoma, Wilms' tumor, testicular tumor, lungcarcinoma including small cell, non-small and large cell lung carcinoma,bladder carcinoma, glioma, astrocyoma, medulloblastoma,craniopharyngioma, ependymoma, pinealoma, retinoblastoma, neuroblastoma,colon carcinoma, rectal carcinoma, hematopoietic malignancies includingall types of leukemia and lymphoma including: acute myelogenousleukemia, acute myelocytic leukemia, acute lymphocytic leukemia, chronicmyelogenous leukemia, chronic lymphocytic leukemia, mast cell leukemia,multiple myeloma, myeloid lymphoma, Hodgkin' s lymphoma, non-Hodgkin' slymphoma.

Cancers treated in certain embodiments also include precancerouslesions, e.g., actinic keratosis (solar keratosis), moles (dysplasticnevi), acitinic chelitis (farmer's lip), cutaneous horns, Barrett'sesophagus, atrophic gastritis, dyskeratosis congenita, sideropenicdysphagia, lichen planus, oral submucous fibrosis, actinic (solar)elastosis and cervical dysplasia.

Cancers treated in some embodiments include non-cancerous or benigntumors, e.g., of endodermal, ectodermal or mesenchymal origin,including, but not limited to cholangioma, colonic polyp, adenoma,papilloma, cystadenoma, liver cell adenoma, hydatidiform mole, renaltubular adenoma, squamous cell papilloma, gastric polyp, hemangioma,osteoma, chondroma, lipoma, fibroma, lymphangioma, leiomyoma,rhabdomyoma, astrocytoma, nevus, meningioma, and ganglioneuroma.

EXAMPLES Example 1 Bifidobacterium animalis ssp. lactis Production

Enriched media is used to grow and prepare Bifidobacterium animalis ssp.lactis for in vitro and in vivo use. For example, media may containsugar, yeast extracts, peptones, trace elements, and vitamins.Alternatively, media may be prepared and Bifidobacterium animalis ssp.lactis grown as shown by Saarela et al., J. Applied Microbiology. 2005.99: 1330-1339, which is hereby incorporated by reference. Influence offermentation time, cryoprotectant and neutralization of cell concentrateon freeze-drying survival, storage stability, and acid and bile exposureof Bifidobacterium animalis ssp. lactis cells produced withoutmilk-based ingredients,

At large scale, the media is sterilized. Sterilization may be by UltraHigh Temperature (UHT) processing. The UHT processing is performed atvery high temperature for short periods of time. The UHT range may befrom 135-180° C. For example, the medium may be sterilized from between10 to 30 seconds at 135° C.

Inoculum can be prepared in flasks or in smaller bioreactors and growthis monitored. For example, the inoculum size may be betweenapproximately 0.5 and 3% of the total bioreactor volume. Depending onthe application and need for material, bioreactor volume can be at least2 L, 10 L, 80 L, 100 L, 250 L, 1000 L, 2500 L, 5000 L, 10,000 L.

Before the inoculation, the bioreactor is prepared and ready with mediumat desired pH, temperature, and oxygen concentration. For example, pHmay be set between 4.5 and 8.0 During the fermentation the pH can becontrolled through the use of sodium hydroxide, potassium hydroxide, orammonium hydroxide. The temperature may be controlled from 25° C. to 45°C., for example at 37° C. Anaerobic conditions are created by reducingthe level of oxygen in the culture broth from around 8 mg/L to 0 mg/L.For example, nitrogen or gas mixtures (N2, CO2, and H2) may be used inorder to establish anaerobic conditions. Alternatively, no gases areused and anaerobic conditions are established by cells consumingremaining oxygen from the medium. Depending on strain and inoculum size,the bioreactor fermentation time can vary. For example, fermentationtime can vary from approximately 5 hours to 48 hours.

Harvesting can be performed by continuous centrifugation. Product willbe resuspended with various excipients to a desired final concentration.Excipients can be added for cryo protection or for protection duringlyophilization. Excipients can include, but are not limited to, sucrose,trehalose, or lactose, and these may be alternatively mixed with bufferand anti-oxidants. Prior to lyophilization, droplets of cell pelletsmixed with excipients are submerged in liquid nitrogen.

Lyophilization of material, including live bacteria, begins with primarydrying. During the primary drying phase, the ice is removed. Here, avacuum is generated and an appropriate amount of heat is supplied to thematerial for the ice to sublime. During the secondary drying phase,product bound water molecules are removed. Here, the temperature israised higher than in the primary drying phase to break anyphysico-chemical interactions that have formed between the watermolecules and the product material. The pressure may also be loweredfurther to enhance desorption during this stage. After the freeze-dryingprocess is complete, the chamber may be filled with an inert gas, suchas nitrogen. The product may be sealed within the freeze dryer under dryconditions, preventing exposure to atmospheric water and contaminants.

Example 2 Orally Administered Bifidobacterium animalis ssp. lactisInhibits Colorectal Carcinoma Tumor Growth

Female 6-8 week old Balb/c mice were obtained from Taconic (Germantown,N.Y.). 100,000 CT-26 colorectal tumor cells (ATCC CRL-2638) wereresuspended in sterile PBS and inoculated in the presence of 50%Matrigel. CT-26 tumor cells were subcutaneously injected into one hindflank of each mouse. When tumor volumes reached an average of 100 mm³(approximately 10-12 days following tumor cell inoculation), animalswere distributed into the following groups: 1) Vehicle+isotype controlantibody IgG2a; and 3) Bifidobacterium animalis ssp. lactis Strain A(ATCC accession number PTA-125097)+IgG2a. Bifidobacterium animalis ssp.lactis bacteria (1×10⁹) were administered by oral gavage (p.o.) daily,starting on day 1 until the conclusion of the study. The Bifidobacteriumanimalis ssp. lactis+IgG2a group showed significant tumor growthinhibition compared to the vehicle+IgG2a group (See FIG. 1).

Example 3 Orally Administered Bifidobacterium animalis ssp. lactisInhibits Colorectal Carcinoma Tumor Growth Comparable to Inhibition SeenWith Anti-PD-1 Treatment

CT-26 tumor cells were subcutaneously injected into one hind flank ofeach Balb/c mouse as above. When tumor volumes reached an average of 100mm³ (approximately 10-12 days following tumor cell inoculation), animalswere distributed into the following groups: 1) Vehicle+PBS; 2)Vehicle+isotype control antibody IgG2a; and 3) Vehicle+anti-PD-1; 4)Bifidobacterium animalis ssp. lactis Strain A (ATCC accession numberPTA-125097)+IgG2a; and 5) Bifidobacterium animalis ssp. lactis StrainA+anti-PD-1. Antibodies were administered intraperitoneally (i.p.) at100 ug/mouse (100 ul final volume) every four days, starting on day 1,and Bifidobacterium animalis ssp. lactis bacteria (1×10⁹) wereadministered by oral gavage (p.o.) daily, starting on day 1 until theconclusion of the study. The Bifidobacterium animalis ssp. lactis+IgG2agroup showed tumor growth inhibition comparable to that seen in thevehicle+anti-PD-1 group (See FIG. 2).

Example 4 Treatment of Colorectal Carcinoma Using DifferentBifidobacterium animalis ssp. lactis Strains

As described in Examples 2 and 3, CT-26 tumor cells were subcutaneouslyinjected into one hind flank of mice and animals were assigned intogroups receiving the following treatments: 1) Vehicle; 2)Bifidobacterium animalis ssp. lactis Strain A (ATCC accession numberPTA-125097); 3) B. animalis lactis Strain B; 4) B. animalis ssp. lactisStrain C; and 5) anti-PD-1. 1×10⁹ bacterial cells were administereddaily (p.o.), beginning on day 1 of animal group assignment, and tumorsmeasured as described above. Anti-PD-1 antibodies were administeredintraperitoneally (i.p.) at 100 ug/mouse (100 ul final volume) everyfour days, starting on day 1. As seen in Table 2, Strain A showedsignificant tumor growth inhibition compared to the other B. animalislactis treatment groups (Table 2 and FIG. 3).

TABLE 2 Colorectal carcinoma tumor volume (mm³) on Day 22 (12^(th) dayof dosing) Anti PD-1 Vehicle Strain C Strain B Strain A Median tumorvol. 1096.97 1775.89 1294.94 1819.68 1788.83 (mm³) Mean tumor vol.1029.97 1757.75 1231.34 1753.12 1704.33 (mm³) SEM (mm³) 193.37 154.75190.00 89.48 119.03

Example 5 Intratumorally Administered Bifidobacterium animalis ssp.lactis Inhibits Colorectal Carcinoma Tumor Growth

As described in Examples 2 and 3, CT-26 tumor cells were subcutaneouslyinjected into one hind flank of mice and animals were assigned intogroups receiving the following treatments: 1) Vehicle; 2)Bifidobacterium animalis ssp. lactis Strain A (ATCC accession numberPTA-125097); and 3) anti-PD-1. 2×10⁹ bacterial cells were administeredintratumorally (IT) on day 1 of animal group assignment, and tumorsmeasured as described above. Mice received a second dose on day 4.Anti-PD-1 antibodies were administered intraperitoneally (i.p.) at 100ug/mouse (100 ul final volume) every four days, starting on day 1. TheBifidobacterium animalis ssp. lactis Strain A group showed significanttumor growth inhibition compared to the control group (See FIG. 4).

Example 6 Bifidobacterium animalis ssp. lactis in a Mouse Melanoma Model

B. animalis ssp. lactis is tested for efficacy in a mouse melanomamodel. For example, Female 6-8 week old C57B1/6 mice are obtained fromTaconic (Germantown, N.Y.). Between 1×10{circumflex over ( )}4 and1×10{circumflex over ( )}6 B16-F10 tumor cells (ATCC CRL-6475) may beused to inoculate various groups of mice. B16-F10 tumor cells may beresuspended in sterile PBS containing 50% Matrigel and inoculated in a100 ul final volume into one hind flank (the first flank) of each mouse.Treatment with Bifidobacterium animalis ssp. lactis is initiated at somepoint following tumor cell inoculation at varied doses and at definedintervals. For example, some mice receive between 1-5×10{circumflex over( )}9 CFU (100 μl final volume) per dose. Possible routes ofadministration include oral gavage (p.o.), intravenous injection,intratumoral injection (IT) or peritumoral or subtumoral or subcutaneousinjection. In order to assess the systemic anti-tumoral effects of B.animalis lactis treatment, additional mice may be inoculated with tumorcells in the contralateral (untreated, second) flank prior to IT,peritumoral, or subtumoral treatment with B. animalis lactis in thefirst flank.

Some mice may receive Bifidobacterium animalis ssp. lactis (p.o.) on day1 (the day following tumor cell injection). Other mice may receive seven(7) consecutive doses of Bifidobacterium animalis ssp. lactis (one doseper day on days 14-21). Other mice receive daily dosing or,alternatively, some mice receive dosing every other day. Alternatively,mice are randomized into various treatment groups at a defined timepoint(e.g. on day 13) or when the tumors reach a certain size (e.g. 100 mm³)and treatment is then initiated accordingly. For example, when tumorvolumes reach an average of 100 mm³ (approximately 10-12 days followingtumor cell inoculation), animals are distributed into groups and treatedwith either vehicle or Bifidobacterium animalis ssp. lactis (p.o. orIT). Some additional groups of mice may be treated with an additionalcancer therapeutic or appropriate control antibody. One example of acancer therapeutic that may be administered is an inhibitor of an immunecheckpoint, for example anti-PD-1, anti-PD-L1, or other treatment thatblocks the binding of an immune checkpoint to its ligand(s). Checkpointinhibitors anti-PD-1 and anti-PD-L1 may be formulated in PBS andadministered intraperitoneally (i.p.) in effective doses. For example,mice are given 100 ug of anti-PD-1 (i.p.) every four days starting onday 1, and continuing for the duration of the study.

In addition, some mice are treated with antibiotics prior to treatment.For example, vancomycin (0.5 g/L), ampicillin (1.0 g/L), gentamicin (1.0g/L) and amphotericin B (0.2 g/L) are added to the drinking water, andantibiotic treatment is halted at the time of treatment or a few daysprior to treatment. Some mice are inoculated with tumor cells withoutreceiving prior treatment with antibiotics. Also, in some groups theB16-f10 cells may be cultured with 100 U/ml penicillin and 10mg/m1streptomycin prior to inoculation.

For example, B16-F10 cells were expanded using standard tissue culturetechnique, maintained in DMEM medium supplemented with 10% fetal bovineserum (FBS), 100 U/ml penicillin, and 10 mg/ml streptomycin in a 37° C.incubator with 5% CO₂. On the day of tumor cell implantation, B16-F10cells were resuspended in cold HBSS at 1×10{circumflex over ( )}6 tumorcells/ml and each mouse was injected with 100 ul of resuspended tumorcells. Tumor growth was measured three times per week using digitalcalipers according to methods known in the art. When the average tumorsize reached approximately 100 mm³, mice were randomly separated intotreatment groups and treatment initiated according to Table 3 below.

TABLE 3 Treatments Group, N = 20 Treatment #1 Treatment #2 1 Vehicle(PO, 100 μL vol. QD) PBS (IP, 100 μL, Q4D) 2 Vehicle (PO, 100 μL vol.QD) anti-PD-L1 (IP, 200 μg/100 μL vol, Q4D) 3 B. animalis ssp. lactisStrain A PBS (IP, 100 μ L, Q4D) (PO, 6.5 × 10{circumflex over ( )}9 CFUin 100 μL vol. QD) 4 B. animalis ssp. lactis Strain A anti-PD-L1 (IP,200 μg/100 μL vol, Q4D) (PO, 6.5 × 10{circumflex over ( )}9 CFU in 100μL vol. QD)

Animals received Treatment #1 (Vehicle or B. animalis ssp. lactis StrainA) via oral gavage every day. Mice received Treatment #2 (PBS oranti-PD-L1 intraperitoneally every 4 days until the termination of thestudy. Treating tumor-inoculated mice with a combination ofBifidobacterium animalis ssp. lactis Strain A and anti-PD-L1 inhibitstumor growth in a manner superior to either B. animalis ssp. lactisStrain A or anti-PD-L1 alone (FIG. 5).

Example 7 Infiltration of CD3+ Cells is Significantly Increased in CT26Tumors in Mice Orally Savaged with B. animalis lactis Strain A

In some studies, at various timepoints, mice are sacrificed and tumors,lymph nodes, or other tissues may be removed for ex vivo flow cytometricanalysis using methods known in the art. For example, tumors aredissociated using a Miltenyi tumor dissociation enzyme cocktailaccording to the manufacturer's instructions. Tumor weights are recordedand tumors are chopped then placed in 15 ml tubes containing the enzymecocktail and placed on ice. Samples are then placed on a gentle shakerat 37° C. for 45 minutes and quenched with up to 15 ml complete RPMI.Each cell suspension is strained through a 70 μm filter into a 50 mlfalcon tube and centrifuged at 1000 rpm for 10 minutes. Cells areresuspended in FACS buffer and washed to remove remaining debris. Ifnecessary, samples are strained again through a second 70 μm filter intoa new tube. Cells are stained for analysis by flow cytometry usingtechniques known in the art. Staining antibodies can include anti-CD11c(dendritic cells), anti-CD80, anti-CD86, anti-CD40, anti-MHCII,anti-CD8a, anti-CD4, and anti-CD103. Other markers that may be analyzedinclude pan-immune cell marker CD45, T cell markers (CD3, CD4, CD8,CD25, Foxp3, T-bet, Gata3, Rorγt, Granzyme B, CD69, PD-1, CTLA-4), andmacrophage/myeloid markers (CD11b, MHCII, CD206, CD40, CSF1R, PD-L1,Gr-1). In addition to immunophenotyping, cytokines are analyzedincluding, but not limited to, IP-10, TNFa, IL-17, IL-13, IL-12p70,IL12p40, IL-10, IL-6, IL-5, IL-4, IL-2, IL-1b, IFNy, GM-CSF, G-CSF,M-CSF, MIG, IP10, MIP1b, RANTES, and MCP-1, using techniques known inthe art. Cytokine analysis may be analyzed on immune cells obtained fromlymph nodes or other tissue, tumor sections, dissociated tumor cells,and/or on purified CD45+ tumor-infiltrated immune cells obtained exvivo. Cytokine levels may be ascertained using various stainingtechniques, qPCR, or other techniques known in the arts.Immunohistochemistry may also be performed on tumor sections to measureT cells, macrophages, dendritic cells, and checkpoint molecule or otherprotein expression using techniques known in the art.

Mice were inoculated with CT26 tumor cells, divided into groups asdescribed above, and orally gavaged with B. animalis ssp. lactis StrainA 8.3×10{circumflex over ( )}9 CFU/mouse daily. Other mice were givenvehicle as a negative control. Mice from this study were sacrificed onday 10 and tumors harvested for analysis. Using known techniquesdescribed above, tumor sections were stained with anti-CD3 antibodies (Tcell marker) to assess the average CD3+ cells per tumor section, andtumor gene expression was analyzed by qPCR using a TaqMan assay asfollows: Tumor RNA was isolated with Qiagen's RNeasy Mini kit (CatalogNo. 74104), using the manufacturer's protocol. cDNA was isolated usingBioRad's iScript™ cDNA Synthesis Kit according to the manufacturer'sprotocol (Catalog No. 1708891). The qPCR reaction was run usingSsoAdvanced™ Universal Probes Supermix 1725281 using manufacturer'sprotocol on the BioRad CFX384 instrument. The TaqMan mouse specificprobes were from Invitrogen, MHC I (b2m) Mm00437762_m1 and β-actinMm01205647_g1 for normalizing gene expression. The delta Ct value foreach tumor was calculated for MHC I using β-actin as the reference gene.The expression for MHC I was calculated using the formula 2{circumflexover ( )}-delta Ct for each mouse tumor and this value was divided byits respective final tumor volume at the end of the study.

Tumor volumes were taken prior to CD3+ immune cell infiltrate and MHCClass I expression analysis. As described in FIG. 1, tumor volume wasnotably decreased on day 9 in the B. animalis ssp. lactis group (FIG.6A). Infiltration of CD3+ immune cells was significantly increased inthe Bifidobacterium animalis ssp. lactis Strain A group relative tovehicle (FIG. 6B), and B. animalis ssp. lactis Strain A induced astriking upregulation of MHC Class I expression (FIG. 6C).

Rather than being sacrificed, some mice may be rechallenged with tumorcell injection into the contralateral flank (or other area) to determinethe impact of the immune system's memory response on tumor growth.

Example 8 Bifidobacterium animalis ssp. lactis in a Mouse Lung CancerModel

Bifidobacterium animalis ssp. lactis is tested for its efficacy in themouse lung cancer model, either alone or in combination with othercancer therapies, including checkpoint inhibitor(s). Mice are dividedinto groups receiving Bifidobacterium animalis ssp. lactis, with orwithout checkpoint inhibitor treatment. As described in Example 6,Bifidobacterium animalis ssp. lactis is administered at varied doses atdefined intervals. For example, some mice receive Bifidobacteriumanimalis ssp. lactis (p.o.) on the day following tumor cell injection(day 1). Some mice receive seven (7) consecutive doses ofBifidobacterium animalis ssp. lactis (one dose per day on days 14-21).Other mice receive daily dosing or, alternatively, some mice receivedosing every other day. Alternatively, mice are randomized into varioustreatment groups at a defined timepoint (e.g. on day 13) or when thetumors reach a certain size (e.g. 100 mm³) and treatment is theninitiated accordingly.

1×10⁶ LLC1 cells, or an appropriate number of lung cancer cells fromanother lung cancer cell line, are injected into the hind flank ofsyngeneic mice. Tumors from the various treatment groups are measuredwith calipers at regular intervals. As described in Example 6, some miceare sacrificed for ex vivo tumor analysis using flow cytometry. Othermice may be rechallenged with tumor cell injection into thecontralateral flank to determine the impact of the immune system'smemory response on tumor growth.

Example 9 Bifidobacterium animalis ssp. lactis in a Mouse Breast CancerModel

Bifidobacterium animalis ssp. lactis is tested for its efficacy in themouse breast cancer model, either alone or in combination with othercancer therapies, including checkpoint inhibitor(s). Mice are dividedinto groups receiving Bifidobacterium animalis ssp. lactis, with orwithout checkpoint inhibitor treatment. As described in Example 6,Bifidobacterium animalis ssp. lactis is administered at varied doses atdefined intervals. For example, some mice receive Bifidobacteriumanimalis ssp. lactis (p.o.) on the day following tumor cell injection(day 1). Some mice receive seven (7) consecutive doses ofBifidobacterium animalis ssp. lactis (one dose per day on days 14-21).Other mice receive daily dosing or, alternatively, some mice receivedosing every other day. Alternatively, mice are randomized into varioustreatment groups at a defined timepoint (e.g. on day 13) or when thetumors reach a certain size (e.g. 100 mm³) and treatment is theninitiated accordingly.

4T1 mouse mammary carcinoma cells are obtained from ATCC and 1×10⁶ cellsin 50 ul PBS are injected subcutaneously into one or both hind limbs ofBalb/c female mice (as described by Wang et al. 2003, Systemicdissemination of viral vectors during intratumoral injection. MolecularCancer Therapeutics; 2(11)). Alternatively, EMT6 mouse mammary carcinomacells are obtained from ATCC and 1×10⁶ cells in 50 μl PBS are injectedsubcutaneously into one or both of the hind limbs of Balb/c female mice6-8 weeks old (as described by Guo et al. 2014, CombinatorialPhotothermal and Immuno Cancer Therapy Using Chitosan-Coated HollowCopper Sulfide Nanoparticles. ASC Nano.; 8(6): 5670-5681). In addition,other available mouse mammary cell lines may be used.

Tumors from the various treatment groups are measured with calipers atregular intervals. As described in Example 6, Bifidobacterium animalisssp. lactis is administered at varied doses at defined intervals. Forexample, some mice are sacrificed for ex vivo tumor analysis using flowcytometry. Other mice may be rechallenged with tumor cell injection intothe contralateral flank to determine the impact of the immune system'smemory response on tumor growth.

Alternatively, 4T1 cells can be used in an orthotopic murine model ofbreast cancer as described by Tao et al. (Tao et al. 2008. Imagable 4T1model for the study of late stage breast cancer. 8: 288). Mice aresacrificed for ex vivo tumor analysis. Tumors are analyzed by flowcytometry and immunohistochemistry.

Example 10 Bifidobacterium animalis ssp. lactis in a Mouse PancreaticCancer Model

Bifidobacterium animalis ssp. lactis is tested for its efficacy in themouse model of pancreatic cancer, either alone or in combination withother cancer therapies, including checkpoint inhibitor(s). Mice aredivided into groups receiving Bifidobacterium animalis ssp. lactis, withor without checkpoint inhibitor treatment. As described in Example 6,some mice receive Bifidobacterium animalis ssp. lactis (p.o.) on the dayfollowing tumor cell injection (day 1). Some mice receive seven (7)consecutive doses of Bifidobacterium animalis ssp. lactis (one dose perday on days 14-21). Other mice receive daily dosing or, alternatively,some mice receive dosing every other day. Alternatively, mice arerandomized into various treatment groups at a defined timepoint (e.g. onday 13) or when the tumors reach a certain size (e.g. 100 mm³) andtreatment is then initiated accordingly.

Panc02 cells are maintained in DMEM, supplemented with 10% fetal calfserum and 1% penicillin/streptomycin, and incubated at 37° C. at 5% CO2.Female 8-10 week-old C57B1/6 mice are obtained from Charles River, Inc.or other certified vendor. Female C57B1/6 mice are injectedsubcutaneously into the right hind flank with 1×10⁶ Panc02 cells. Thisprotocol is based on standard Panc02 tumor models (Maletzki et al. 2008.Pancreatic cancer regression by intratumoral injection of livestreptococcus pyogenes in a syngeneic mouse model. Gut. 57:483-491).Tumors from the various treatment groups are measured with calipers atregular intervals. As described in Example 6, some mice are sacrificedfor ex vivo tumor analysis using flow cytometry, while other mice arerechallenged to determine the impact of the memory response on tumorgrowth.

Alternatively, Panc02, 6606PDA, or Capan-1 cells lines can be used in anorthotopic murine model of pancreatic cancer as described by Partecke etal. (Partecke et al. 2011. A syngeneic orthotopic murine model ofpancreatic adenocarcinoma in the C57/B16 mouse using the Panc02 and6606PDA cell lines. Eur. Surg. Res. 47(2):98-107) or Chai et al. (Chaiet al. 2013. Bioluminescent orthotopic model of pancreatic cancerprogression. J. Vis. Exp. 76: 50395). Mice are sacrificed for ex vivotumor analysis. Tumors are analyzed by flow cytometry andimmunohistochemistry.

Example 11 Bifidobacterium animalis ssp. lactis in a Mouse Model ofHepatocellular Carcinoma

Bifidobacterium animalis ssp. lactis is tested for its efficacy in themouse model of hepatocellular carcinoma, either alone or in combinationwith other cancer therapies, including checkpoint inhibitor(s). Mice aredivided into groups receiving Bifidobacterium animalis ssp. lactis, withor without checkpoint inhibitor treatment. As described in Example 6,Bifidobacterium animalis ssp. lactis is administered at varied doses atdefined intervals. For example, some mice receive Bifidobacteriumanimalis ssp. lactis (p.o.) on the day following tumor cell injection(day 1). Some mice receive seven (7) consecutive doses ofBifidobacterium animalis ssp. lactis (one dose per day on days 14-21).Other mice receive daily dosing or, alternatively, some mice receivedosing every other day. Alternatively, mice are randomized into varioustreatment groups at a defined timepoint (e.g. on day 13) or when thetumors reach a certain size (e.g. 100 mm³) and treatment is theninitiated accordingly.

Hepatocellular carcinoma is induced in mice by subcutaneous inoculationof 1×10⁶ Hepa129 cells (obtained from NCI or other source), or anappropriate number of cells from other hepatocellular carcinoma cellline (as described by Gonzalez-Carmona et al. 2008. CD40 ligand-expressing dendritic cells induce regression of hepatocellular carcinoma byactivating innate and acquired immunity in vivo. Hepatology.48(1):157-168). Tumor cells are inoculated into one or both flanks.Tumors from the various treatment groups are measured with calipers atregular intervals. As described in Example 6, some mice are sacrificedfor ex vivo tumor analysis using flow cytometry, while other mice arerechallenged to determine the impact of the memory response on tumorgrowth.

Example 12 Bifidobacterium animalis ssp. lactis in a Mouse LymphomaModel

Bifidobacterium animalis ssp. lactis is tested for its efficacy in themouse model of lymphoma, either alone or in combination with othercancer therapies, including checkpoint inhibitor(s). Mice are dividedinto groups receiving Bifidobacterium animalis ssp. lactis, with orwithout checkpoint inhibitor treatment. As described in Example 6,Bifidobacterium animalis ssp. lactis is administered at varied doses atdefined intervals. For example, some mice receive Bifidobacteriumanimalis ssp. lactis (p.o.) on the day following tumor cell injection(day 1). Some mice receive seven (7) consecutive doses ofBifidobacterium animalis ssp. lactis (one dose per day on days 14-21).Other mice receive daily dosing or, alternatively, some mice receivedosing every other day. Alternatively, mice are randomized into varioustreatment groups at a defined timepoint (e.g. on day 13) or when thetumors reach a certain size (e.g. 100 mm³) and treatment is theninitiated accordingly.

One lymphoma cell line is the A20 lymphoma, although other lymphoma celllines may be used with syngeneic mice. A20 lymphoma cells are obtainedfrom ATCC and 5×10⁶ cells in 50 ul PBS are injected subcutaneously intoone or both of the hind limbs of Balb/c female mice (as described byHouot et al. 2009. T-cell modulation combined with intratumoral CpGcures lymphoma in a mouse model without the need for chemotherapy.Blood. 113(15): 3546-3552). Tumors from the various treatment groups aremeasured with calipers at regular intervals. As described in Example 6,some mice are sacrificed for ex vivo tumor analysis using flowcytometry, while other mice are rechallenged to determine the impact ofthe memory response on tumor growth.

Example 13 Bifidobacterium animalis ssp. lactis in a Mouse ProstateCancer Model

Bifidobacterium animalis ssp. lactis is tested for its efficacy in themouse model of prostate cancer, either alone or in combination withother cancer therapies, including checkpoint inhibitor(s). Mice aredivided into groups receiving Bifidobacterium animalis ssp. lactis, withor without checkpoint inhibitor treatment. As described in Example 6,Bifidobacterium animalis ssp. lactis is administered at varied doses atdefined intervals. For example, some mice receive Bifidobacteriumanimalis ssp. lactis (p.o.) on the day following tumor cell injection(day 1). Some mice receive seven (7) consecutive doses ofBifidobacterium animalis ssp. lactis (one dose per day on days 14-21).Other mice receive daily dosing or, alternatively, some mice receivedosing every other day. Alternatively, mice are randomized into varioustreatment groups at a defined timepoint (e.g. on day 13) or when thetumors reach a certain size (e.g. 100 mm³) and treatment is theninitiated accordingly.

Mouse prostate cancer cells (1×10⁵ RM-1 cells or an appropriate numberof cells from another prostate cancer cell line) are injected intosyngeneic mice. Tumors from the various treatment groups are measuredwith calipers at regular intervals. As described in Example 6, some miceare sacrificed for ex vivo tumor analysis using flow cytometry, whileother mice are rechallenged to determine the impact of the memoryresponse on tumor growth.

Example 14 Bifidobacterium animalis ssp. lactis in a Mouse PlasmacytomaModel

Bifidobacterium animalis ssp. lactis is tested for its efficacy in themouse model of plasmacytoma, either alone or in combination with othercancer therapies, including checkpoint inhibitor(s). Mice are dividedinto groups receiving Bifidobacterium animalis ssp. lactis, with orwithout checkpoint inhibitor treatment. As described in Example 6,Bifidobacterium animalis ssp. lactis is administered at varied doses atdefined intervals. For example, some mice receive Bifidobacteriumanimalis ssp. lactis (p.o.) on the day following tumor cell injection(day 1). Some mice receive seven (7) consecutive doses ofBifidobacterium animalis ssp. lactis (one dose per day on days 14-21).Other mice receive daily dosing or, alternatively, some mice receivedosing every other day. Alternatively, mice are randomized into varioustreatment groups at a defined timepoint (e.g. on day 13) or when thetumors reach a certain size (e.g. 100 mm³) and treatment is theninitiated accordingly.

Mineral Oil Induced Model of Plasmacytoma

To examine the efficacy of Bifidobacterium animalis ssp. lactis in aplasmacytoma or multiple myeloma model, mice are injectedintraperitoneally three times with 500 ul of2,6,10,12-tetramethylpentadecane (“pristane oil”) at various time pointsbetween 0 and 60 days, as described by Potter et al. 1983. Peritonealplasmacytomagenesis in mice: comparison of different pristane doseregimens. J. Natl. Cancer Inst. 71(2):391-5 (see also Lattanzio et al.1997. Defective Development of Pristane-Oil Induced Plasmacytomas inInterleukin-6-Deficient BALB/C Mice. Am. J. Pathology: 151(3):689696).Progression of disease is measured by the degree of abdominal swellingand immune cells and particles in the ascites. Ascites fluid is analyzedfor immune cell phenotype by flow cytometry as described in Example 2.

Cell-Line Induced Model of Plasmacytoma

To examine the efficacy of Bifidobacterium animalis ssp. lactis in aplasmacytoma or multiple myeloma model, either MOPC-104E cells or J558plasmacytoma cells (TIB-6 ATCC) are injected subcutaneously into one ormore hind flanks of Balb/c mice (5×10⁶ cells), based on model describedby Bhoopalam et al. 1980. Effect of dextran-S (alpha, 1-3 dextran) onthe growth of plasmacytomas MOPC-104E and J558. J. Immunol.125(4):1454-8 (see also Wang et al. 2015. IL-10 enhances CTL-mediatedtumor rejection by inhibiting highly suppressive CD4+ T cells andpromoting CTL persistence in a murine model of plasmacytoma.Oncolmmunology. 4(7): e1014232-1-9). Mice are divided into groupsreceiving Bifidobacterium animalis ssp. lactis by oral gavage, and withor without checkpoint inhibitor treatment. Tumors from the varioustreatment groups are measured with calipers at regular intervals. Asdescribed in Example 6, some mice are sacrificed for ex vivo tumoranalysis using flow cytometry, while other mice are rechallenged todetermine the impact of the memory response on tumor growth.

Example 15 Bifidobacterium animalis ssp. lactis in a SCID Mouse Model ofMouse Myeloma

Bifidobacterium animalis ssp. lactis is tested for its efficacy in theSCID mouse model of myeloma, either alone or in combination with othercancer therapies, including checkpoint inhibitor(s). Mice are dividedinto groups receiving Bifidobacterium animalis ssp. lactis, with orwithout checkpoint inhibitor treatment. As described in Example 6,Bifidobacterium animalis ssp. lactis is administered at varied doses atdefined intervals. For example, some mice receive Bifidobacteriumanimalis ssp. lactis (p.o.) on the day following tumor cell injection(day 1). Some mice receive seven (7) consecutive doses ofBifidobacterium animalis ssp. lactis (one dose per day on days 14-21).Other mice receive daily dosing or, alternatively, some mice receivedosing every other day. Alternatively, mice are randomized into varioustreatment groups at a defined timepoint (e.g. on day 13) or when thetumors reach a certain size (e.g. 100 mm³) and treatment is theninitiated accordingly.

To examine the efficacy of Bifidobacterium animalis ssp. lactis using ahuman plasma cell leukemia, 1×10⁷ human myeloma cell lines, ARH77 cells(ARH77-ATCC CRL-1621, or an appropriate number of cells from anothermyeloma cell line such as KPMM2) are used. Myeloma cells are injectedsubcutaneously into one or both hind flanks of SCID mice (See Caers etal. 2004. Of mice and men: disease models of multiple myeloma. DrugDiscovery Today: Disease Models. 1(4):373-380. Tumors from the varioustreatment groups are measured with calipers at regular intervals. Asdescribed in Example 6, some mice are sacrificed for ex vivo tumoranalysis using flow cytometry, while other mice are rechallenged todetermine the impact of the memory response on tumor growth.

Example 16 Bifidobacterium animalis ssp. lactis in a mouse renal cellcarcinoma model

Bifidobacterium animalis ssp. lactis is tested for its efficacy in themouse model of renal cell carcinoma, either alone or in combination withother cancer therapies, including checkpoint inhibitor(s). Mice aredivided into groups receiving Bifidobacterium animalis ssp. lactis, withor without checkpoint inhibitor treatment. As described in Example 6,Bifidobacterium animalis ssp. lactis is administered at varied doses atdefined intervals. For example, some mice receive Bifidobacteriumanimalis ssp. lactis (p.o.) on the day following tumor cell injection(day 1). Some mice receive seven (7) consecutive doses ofBifidobacterium animalis ssp. lactis (one dose per day on days 14-21).Other mice receive daily dosing or, alternatively, some mice receivedosing every other day. Alternatively, mice are randomized into varioustreatment groups at a defined timepoint (e.g. on day 13) or when thetumors reach a certain size (e.g. 100 mm³) and treatment is theninitiated accordingly.

To examine the efficacy of Bifidobacterium animalis ssp. lactis in amouse model of renal cell carcinoma, Renca cells (ATCC CRL-2947) orother renal cell carcinoma cells are injected subcutaneously into one orboth flanks of 7-8 week old syngeneic Balb/c mice (5×10⁶ in 0.1 ml PBS).Tumors from the various treatment groups are measured with calipers atregular intervals. As described in Example 6, some mice are sacrificedfor ex vivo tumor analysis using flow cytometry, while other mice arerechallenged to determine the impact of the memory response on tumorgrowth.

Example 17 Bifidobacterium animalis ssp. lactis in a Mouse BladderCancer Model

Bifidobacterium animalis ssp. lactis is tested for its efficacy in themouse model of bladder cancer, either alone or in combination with othercancer therapies, including checkpoint inhibitor(s). Mice are dividedinto groups receiving Bifidobacterium animalis ssp. lactis, with orwithout checkpoint inhibitor treatment. As described in Example 6,Bifidobacterium animalis ssp. lactis is administered at varied doses atdefined intervals. For example, some mice receive Bifidobacteriumanimalis ssp. lactis (p.o.) on the day following tumor cell injection(day 1). Some mice receive seven (7) consecutive doses ofBifidobacterium animalis ssp. lactis (one dose per day on days 14-21).Other mice receive daily dosing or, alternatively, some mice receivedosing every other day. Alternatively, mice are randomized into varioustreatment groups at a defined timepoint (e.g. on day 13) or when thetumors reach a certain size (e.g. 100 mm³) and treatment is theninitiated accordingly.

On the day of inoculation, MBT-2 cells (or other bladder cancer cellline) are harvested and resuspended in 1:1 PBS/Matrigel mixture. 2×10⁵MBT-2 cells are suspended in 100 ul of mixture and injectedsubcutaneously into one or both hind flanks of syngeneic mice. Tumorsare measured with calipers at regular intervals.

As described in Example 6, some mice are sacrificed for ex vivo tumoranalysis using flow cytometry, while other mice are rechallenged todetermine the impact of the memory response on tumor growth.

Example 18 The Efficacy of a Bifidobacterium animalis ssp. lactis Strainis Compared to Other Bifidobacterium Strains for Efficacy in CancerModels

Using methods described above, various Bifidobacterium animalis ssp.lactis and other Bifidobacterium strains are tested and compared forefficacy in various cancer models. Such models may include, but are notlimited to, melanoma, lung cancer, breast cancer, colon cancer,colorectal cancer, pancreatic cancer, hepatocellular cancer, lymphoma,prostate cancer, plasmacytoma, a SCID model of myeloma, renal cellcarcinoma, and/or bladder cancer.

Example 19 An Open-Label Study of the Safety, Tolerability and Efficacyof a Bifidobacterium animalis ssp. lactis Strain A Oral Therapeutic inPatients with Metastatic Colorectal Carcinoma

A multi-center, open-label clinical study with dose escalations and doseexpansions to assess preliminary safety, tolerability, and efficacy ofthe Bifidobacterium animalis ssp. lactis Strain A is performed. Thestudy proceeds in three parts: Part A: Dose escalation in microsatellitestable (MSS) metastatic colorectal carcinoma (CRC) and alternativeindications, Part B: MSS CRC and alternative indications, and Part C:microsatellite instable (MSI) CRC. Dose escalation occurs in a standard3+3 design. In part A, from 9 to 18 patients are enrolled. Parts B and Care enrolled concurrently. In Part B, up to 15 and no fewer than 10pateints are enrolled. In Part C no fewer than 5 and up to 10 patientsare enrolled. Based on in vivo studies of allograft bearing mice, anexemplary estimated human effective dose is 2×10¹¹ organisms per day,delivered per enteric capsule. A schematic overview of the study isdepicted in FIG. 7.

The primary objectives of the study include the determination of themaximum tolerated dose within the tested dose range for Bifidobacteriumanimalis ssp. lactis Strain A in patients wiuth advanced malignancies;the determination of the recommended phase 2 dose for Bifidobacteriumanimalis ssp. lactis Strain A in CRC; the evaluation of the safety andtolerability, including dose limiting toxicities of Bifidobacteriumanimalis ssp. lactis Strain; and the demonstration of anti-tumoractivity of Bifidobacterium animalis ssp. lactis Strain A in patientswith CRC (MSI and MSS). The anti-tumor activity will be assessed bymonitoring changes in circulating tumor cells, immune cell subsets inblood and tumor, and tumor viability; objective response rate andduration of response; progression-free survival; overall survival;clinical benefit rate and duration of clinical benefit rate; and diseasecontrol rate and duration of disease control rate. The secondaryobjective is to determine the human distribution and elimination ofBifidobacterium animalis ssp. lactis Strain A. The exploratoryobjectives is to evaluate correlations of Bifidobacterium animalis ssp.lactis Strain A response with molecular markers relevant to each tumortype and to identify possible mechanisms of resistance toBifidobacterium animalis ssp. lactis Strain A.

Inclusion and Exclusion Criteria:

The inclusion criteria for all parts of the study include the following:

-   -   1. Written informed consent obtained prior to any screening        procedures and in accordance with federal, local, and        institutional guidelines.    -   2. Age≥18 years.    -   3. Adequate hepatic function:        -   a. total bilirubin≤2 times the upper limit of normal (ULN)            (except patients with Gilbert's syndrome [hereditary            indirect hyperbilirubinemia] who must have a total bilirubin            of ≤3 times ULN),        -   b. aspartate aminotransferase (AST) and alanine            aminotransferase (ALT)≤2.5 times ULN (except patients with            known liver involvement of their tumor who must have their            AST and ALT≤5.0 times ULN).    -   4. Adequate renal function: estimated creatinine clearance of        ≥30 mL/min, calculated using the formula of Cockcroft and Gault        (140-Age)·Mass (kg)/(72·creatinine mg/dL); multiply by 0.85 if        female.    -   5. All patients in part B+C must be willing to have fresh        biopsies at start of therapy and after 4 weeks of therapy.    -   6. Contraception: Female patients of child-bearing potential        must agree to use dual methods of contraception (including one        highly effective and one effective method of contraception) and        have a negative serum pregnancy test at Screening, and male        patients must use an effective barrier method of contraception        if sexually active with a female of child-bearing potential. For        both male and female patients, effective methods of        contraception must be used throughout the study and for 3 months        following the last dose.

For the portions of the study testing relapsed/refactory colorectalcancer, the inclusion criteria also include the following:

-   -   7. Histological or cytological documentation of adenocarcinoma        of the colon or rectum.    -   8. Known MSI/MSS status.    -   9. Measurable disease by RECIST v1.1.    -   10. Metastatic disease not suitable for upfront curative-intent        surgery.    -   11. Documented evidence of progressive disease according to        RECIST v1.1.    -   12. Prior treatment (with completion of a course of therapy, or        to disease progression or intolerability) with each of the        following:        -   a. Fluoropyrimidine-, oxaliplatin-, irinotecan-based            chemotherapies (e.g., FOLFOX and FOLFIRI)        -   b. if KRAS wild-type, an anti-EGFR therapy,        -   c. Regorafenib or TAS 102 (Past A required, parts B+C            optional)        -   d. Radiation and surgery are not considered as prior            anticancer regimens    -   13. Patients should not be transfusion dependent.    -   14. Adequate hematopoietic function: ANC≥1000/mm3, hemoglobin        (Hb)≥9.0 g/dL, and platelet count≥100,000/mm3.    -   15. Eastern Cooperative Oncology Group (ECOG) performance status        of ≤1.    -   16. Life expectancy of ≥3 months.

The following categories of patient are excluded from the study:

-   -   1. Female patients who are pregnant or lactating.    -   2. Major surgery within 4 weeks before C1D1.    -   3. Impaired cardiac function or clinically significant cardiac        diseases, including any of the following:        -   a. Unstable angina or acute myocardial infarction ≤3 months            prior to C1D1;        -   b. Clinically significant heart disease (e.g., symptomatic            congestive heart failure [e.g., >NYHA Class 2]; uncontrolled            arrhythmia, or hypertension; history of labile hypertension            or poor compliance with an antihypertensive regimen).    -   4. Uncontrolled active severe systemic infection requiring        parenteral antibiotics, antivirals, or antifungals within one        week prior to C1D1.    -   5. Any ongoing antibiotic treatment which has not been        discontinued at least 3 daus prior to initiation of therapy    -   6. Patients with known symptomatic brain metastasis are not        suitable for enrollment. Patients with asymptomatic, stable,        treated brain metastases are eligible for study entry.    -   7. Patients with a known history of human immunodeficiency virus        (HIV); HIV testing is not required as part of this study.    -   8. Known, active hepatitis A, B, or C infection; or known to be        positive for HCV RNA or HBsAg (HBV surface antigen).    -   9. Prior malignancies:        -   a. Patients with adequately resected basal or squamous cell            carcinoma of the skin, or adequately resected carcinoma in            situ (i.e. cervix) may enroll irrespective of the time of            diagnosis.        -   b. Prior malignancies which may interfere with the            interpretation of the study. Cancer treated with curative            intent<5 years previously will not be allowed unless            approved by the Sponsor. Cancer treated with curative            intent>5 years previously and without evidence of recurrence            will be allowed.    -   10. Patients with active central nervous system (CNS)        malignancy. Patients who have only had prophylactic intrathecal        or intravenous chemotherapy against CNS disease are eligible.    -   11. Patients with gastrointestinal tract disease (or        uncontrolled vomiting or diarrhea) that could interfere with the        absorption of EVP001.    -   12. Serious psychiatric or medical conditions that, in the        opinion of the Investigator, could interfere with treatment,        compliance, or the ability to give consent.    -   13. Patients unwilling to comply with the protocol including        required biopsies and sample collections required to measure        disease.    -   14. Radiotherapy within two weeks prior to screening. Patients        must have recovered from clinically significant toxicities.

The use of any concomitant medication/therapy, includingover-the-counter (OTC) medications deemed necessary for the care of thepatient is permitted during the study. Medications required to treatAEs, manage cancer symptoms, concurrent stable diseases and supportivecare agents (e.g. blood product transfusions), pain medications,anti-emetics, and anti-diarrheals are allowed. Concurrent therapy withgrowth factors is allowed. The use of any immunosuppressive agents mustbe discussed between the Investigator and the Medical Monitor on acase-by-case basis. Any diagnostic, therapeutic, or surgical procedureperformed during the study period should be recorded, including thedates, description of the procedure(s), and any clinical findings, ifapplicable. All antibiotics are contraindicated.

Hormonal contraceptives are permitted in women of child-bearingpotential. Hormonal contraceptives include any marketed contraceptiveagent that includes an estrogen and/or a progestational agent.

Investigational or commercial anticancer agents other thanBifidobacterium animalis ssp. lactis Strain A is not allowed during thestudy. The initiation of any non-protocol specific anti-tumor treatmentis considered an indication of disease relapse/progression and should berecorded appropriately in the electronic case report forms.

Palliative radiation therapy to non-target lesions is permitted butstudy treatment is held for ≥1 day before the start of palliativeradiation therapy and ≥1 day following each dose of palliative radiationtherapy. Treatment with Bifidobacterium animalis ssp. lactis Strain A isnot discontinued solely due to palliative radiation.

Supportive measures for optimal medical care should be provided topatients during participation in this study. These should be based oninstitutional and/or National Comprehensive Cancer Network (NCCN)guidelines.

Dose Escalation Study

Patients receive all Bifidobacterium animalis ssp. lactis Strain A dosesduring the 7 day treatment period, or have had a dose-limiting toxicity(DLT) within the treatment period to be considered evaluable for doseescalation decisions. Bifidobacterium animalis ssp. lactis Strain A isorally administered as tablets or enteric coated capsules. Doseescalation decisions occur when the cohort of patients has met thesecriteria.

A DLT is defined as an adverse event (AE) or abnormal laboratory valuethat occurs within the first 7 days of treatment with Bifidobacteriumanimalis ssp. lactis Strain A, except for those that are clearly andincontrovertibly due to underlying disease, disease progression, orextraneous causes, and meets any of the criteria included in Table 4.National Cancer Institute Common Terminology Criteria for Adverse Events(NCI CTCAE) (Version 4.03) is used for all grading. In addition, >4missed doses of Bifidobacterium animalis ssp. lactis Strain A will beconsidered a DLT. Dose escalation decisions occur when the cohort ofpatients has met these criteria.

TABLE 4 Criteria for defining DLT Toxicity Any of the following criteria(based on CTCAE [Version 4.03]): Non-Hematologic Grade ≥3nausea/vomiting, while taking optimal supportive medications. Any otherGrade ≥3 non-hematological toxicity except alopecia or electrolyteabnormalities correctable with supportive therapy. Hematologic Grade 4neutropenia lasting more than 5 days. Febrile neutropenia (absoluteneutrophil count [ANC] <1 × 10⁹/L, fever >38.5° C.). Grade 4thrombocytopenia, or Grade 3 thrombocytopenia with bleeding, or anyrequirement for platelet transfusion. CTCAE Version 4.03 will be usedfor grading all AEs and laboratory abnormalities. Patients may receivesupportive care as per local institutional guidelines.

To implement dose escalation decisions, the available toxicityinformation (i.e., all AEs and all laboratory abnormalities regardlessof DLT assessment) is evaluated by the enrolling Investigators andSponsor medical monitor at a dose decision meeting or teleconference.Decisions are based on an evaluation of all relevant data available fromall dose cohorts evaluated in the ongoing study including safetyinformation, DLTs, all NCI CTCAE, Version 4.03 toxicity data duringCycle 1 from evaluable patients. Drug administration at the next higherdose cohort may not proceed until the Investigator receives writtenconfirmation from Sponsor indicating that the results of the previousdose cohort were evaluated and that it is permissible to proceed to thenext higher dose cohort.

Table 5 below describes the starting dose and the dose levels that maybe evaluated during the study for all parts of the study.

TABLE 5 Bifidobacterium animalis ssp. lactis Strain A Dose EscalationLevels Dose Levels Cohort QD dosing; 3 week cycles Number of Patients 12 × 10⁸ organisms 3 + 3 2 1 × 10⁹ organisms 3 + 3 3 2 × 10⁹ organisms3 + 3 4 (optional) 4 × 10⁹ organisms 3

A standard 3+3 dose escalation is conducted as follows:

-   -   If 0 of 3 patients experiences a DLT, escalate to next higher        dose cohort.    -   If 1 of 3 patients experiences a DLT, that cohort will be        expanded to 6 patients. If 1 of 6 patients experiences a DLT,        escalate to the next higher dose cohort;    -   If ≥2 of 3 or ≥2 of 6 patients experience a DLT, the maximum        tolerated dose (MTD) is exceeded.    -   If the MTD is exceeded, enrollment of additional patients will        be at a lower dose level. If a starting dose does not clear DLT        assessment, dose de-escalation will proceed using standard 3+3        rules

Intra-patient dose escalations are permitted for all cohorts after theintended dose level has been shown to be safe (i.e., all patientstreated at the intended dose level completed DLT assessments and ≤1patient experienced a DLT).

For dose escalation patients after 7 days and dose expansion patients,if an event meeting the definition of a DLT, but without necessarilyoccurring within the first 21 days, is observed in >33% of patients atany time, or if >33% of treated patients have withdrawn consent due totoxicity, enrollment will be held and a meeting with all Investigatorsand Sponsor will take place to review the events and discuss theirclinical significance. Based on this review, the Sponsor may elect toreduce the dose for enrolled patients and to resume enrollment of theexpansion cohort at this lower dose, or the enrollment into theexpansion cohort may be stopped.

Safety and tolerability are evaluated by means of DLTs (dose escalationcohorts only), AE reports, physical examinations, electrocardiograms andlaboratory safety evaluations.

Anti-tumor activity are assessed by the Investigator according todisease specific response criteria and described in terms of objectiveresponse rate, duration of response, progression-free survival, clinicalbenefit rate, overall survival, and disease control rate.

In Part A: Peripheral blood WBC subsets and cytokines are analyzed atbaseline and 7 days. Cytokines are additionally analyzed at 24 and 48hours.

In Parts B and C: Peripheral blood WBC subsets and cytokines areanalyzed at baseline and 7 and 21 days. Baseline and day 28 tumorbiopsies are analyzed for immune subset infiltration, as well as makersof angiogenesis, proliferation, and death.

Patients continue to receive Bifidobacterium animalis ssp. lactis StrainA until the patient has confirmed pharmacodynamics, withdraws consent,is lost to follow-up, experiences intolerable toxicity which precludesfurther treatment with Bifidobacterium animalis ssp. lactis Strain A, ortreatment is discontinued at the discretion of the patient,Investigator, or Sponsor. Patients who have objective diseaseprogression but have evidence of overall clinical benefit may, at therequest of the treating physician, continue treatment withBifidobacterium animalis ssp. lactis Strain A after discussion with theMedical Monitor.

Example 20 Intratumorally Administered Bifidobacterium animalis ssp.lactis Inhibits Colorectal Carcinoma Tumor Growth

As described in Examples 2 and 3, CT-26 tumor cells were subcutaneouslyinjected into one hind flank of mice and animals were assigned intogroups receiving the following treatments: 1) Sucrose Vehicle; 2)anti-PD-1 and anti-CTLA4; and 3) Bifidobacterium animalis ssp. lactisStrain A, anti-PD-1, and anti-CTLA4. 2x10⁹ bacterial cells wereadministered by oral gavage (p.o.) every day for 21 days. Anti-PD-1antibodies were administered intraperitoneally (i.p.) at 200 ug/mouse(100 ul final volume) every four days, starting on day 1, six times intotal. Anti-CTLA4 antibodies were administered intraperitoneally (i.p.)at 100 ug/mouse (100 ul final volume) every four days, starting on day1, six times in total. The tumor volumes were measured as describedabove. The triple combination group of Bifidobacterium animalis ssp.lactis Strain A, anti-PD-1, and anti-CTLA4 showed significant tumorgrowth inhibition compared to the control group and anti-PD-1 andanti-CTLA4 group (See FIG. 8).

Example 21 Genomic Analysis of Bifidobacterium animalis ssp. LactisStrain A

Over the duration of a CT26 model experiments as described above, tumorvolume varied when some stains of Bifidobacterium animalis ssp. Lactiswere administered. Negative performing microbes were determined througha three-way comparison of tumor volumes at termination of groups treatedwith microbes, anti-PD1, and vehicle. The distributions of tumor volumesat termination of the anti-PD1 group vs. the vehicle group were used asa benchmark to classify negative performance of microbes. If thedistributions were more closely overlaid with vehicle than the grouptreated with anti-PD1, the strain was considered a negative performingmicrobe.

For example, tumor volume was found to be higher for groups treated withtwo species of Bifidobacterium animalis lactis, Strain B and Strain C,compared to the group treated with Strain A.

Consistent with these findings, a comparison of in vitro signatures ofthe three strains from a mouse dendritic cell assay show that Strain Aexhibits an immune profile with a decreased induction of pro-tumorigeniccytokines compared to Strain B and Strain C (see FIGS. 9A and 9B).Several of these cytokines have been found to be associated with poorerprognosis in the serum of CRC patients (Mager et al., (2016)Cytokine-Induced Modulation of Colorectal Cancer. Frontiers in Oncology.6. 96. 10.3389).

To elucidate the differences between the strains, Stains A, B, and Cwere sequenced to ˜500× using Illumina MiSeq. The complete and circularStrain A genome (Table 1) was used as the reference to call singlenucleotide polymorphisms (SNPs) between the strains. Coding regions werepredicted, and SNPs that occurred in coding regions were recorded, alongwith the nature of the coding change (synonymous, missense, frameshift,ect.) Using groupings established through results in the CT26 tumormodel, SNPs that were present in negative strains (Strains B and C) whencompared to the reference Strain A were identified, and structuresunique to positive strains (e.g., Strain A) were identified.

When compared to highly homologous non-efficacious strains, Strain Acontains single nucleotide polymorphisms (SNPs) and orinsertion/deletion events in the following genes listed in Tables 6 and7.

TABLE 6 SNPs and/or insertion/deletions in Strain Acompared to non-efficacious strains Strain  Posi- Strain A tion A AminoType of in Base Acid gene product Variant Gene change change glcUputative  Missense  301 C Arg glucose uptake  protein  GlcU glcUputative  Missense  814 C Pro glucose uptake  protein  GlcU relA Bi-Missense  251 G Gly func- tional (p)ppGpp synthase/ hydrolase RelA relABi- Missense 2053 G Val func- tional (p)ppGpp synthase/ hydrolase RelAmetF 5,10- Missense  527 T Phe methylene- tetrahy- drofolate  reductasennr Bi- Missense  574 C Pro func- tional NAD(P)H- hydrate repair  enzyme Nnr ykoE_1 Putative Missense  533 C Ala HMP/ thiamine permease  proteinYkoE tcrY putative  Missense  300 G Gln sensor histidine  kinase TcrYtcrY putative  Missense   49 C Pro sensor histidine  kinase TcrY dacD-alanyl- Frame-  199 DELETION His D-alanine shift carboxy- peptidasehypo- hypothe-  Missense  739 A Ile theti- tical cal protein pro- teinhypo- hypothe- Frame-  990 DELETION His theti- tical  shift cal proteinpro- tein rdgB dITP/XTP Missense  547 A Ser pyrophos- phatase hypo-hypothe-  Missense  290 C Ala theti- tical cal protein pro- tein glnBNitrogen  Missense  161 A Asp regula- tory protein  P-II accC Biotin Frame-  826 DELETION — carboxy- shift lase trxB_2 Thiore- Missense  926T Val doxin reduc- tase afsK Serine/ Missense  686 G Gly threonine-protein  kinase  AfsK nhaK Sodium,  Missense  989 T Val potassium,lithium  and rubidium/ H(+) antiporter hypo- hypothe- Inframe_   45-INSERTION — theti- tical  Inser-   77 (GGCGCTCGGC cal protein tionACCCTGGCGAT pro- TGGCGCGGCA tein AC)(SEQ  ID NO: 2) oxc_1 Oxalyl- Frame- 183- DELETION — CoA shift  184 decar-   boxylase wbgU UDG-N- Missense   7 G Val acetyl- glucosa- mine 4- epimerase wcaJ UDP- Missense  292 GGly glucose: undeca- prenyl- phosphate glucose- 1-phosphate transferasehypo- Hypotheti- Inframe_  126- DELETION — theti- cal  Deletion  128 calprotein pro- tein yciV 5′-3′ Missense  100 T Ser exoribo- nuclease aspAAspartate  Missense 1355 C Ala ammonia- lyase tcrY putative  Missense 368 T Phe sensor histidine  kinase TcrY tcrY putative  Missense  278 CPro sensor histidine  kinase TcrY nagC_2 N- Missense  457 G Ala acetyl-glucosamine repressor

TABLE 7 Genes with synonymous variants Position Strain A Strain A inBase Amino Acid gene product Gene change change hypotheticalhypothetical protein 753 T Leu protein hemN Oxygen-independent 912 A Glycoproporphyrinogen- III oxidase-like protein hypothetical hypotheticalprotein 951 G Pro protein hypothetical hypothetical protein 1722 T Proprotein cytR_2 HTH-type 372 C Ile transcriptional repressor CytR egtCGamma-glutamyl- 135 C Ile hercynylcysteine sulfoxide hydrolasehypothetical hypothetical protein 30 G Arg protein

INCORPORATION BY REFERENCE

All publications patent applications mentioned herein are herebyincorporated by reference in their entirety as if each individualpublication or patent application was specifically and individuallyindicated to be incorporated by reference. In case of conflict, thepresent application, including any definitions herein, will control.

EQUIVALENTS

Those skilled in the art will recognize, or be able to ascertain usingno more than routine experimentation, many equivalents to the specificembodiments of the invention described herein. Such equivalents areintended to be encompassed by the following claims.

LENGTHY TABLES The patent application contains a lengthy table section.A copy of the table is available in electronic form from the USPTO website(https://seqdata.uspto.gov/?pageRequest=docDetail&DocID=US20210093680A1).An electronic copy of the table will also be available from the USPTOupon request and payment of the fee set forth in 37 CFR 1.19(b)(3).

What is claimed is: 1-133. (canceled)
 134. A method of treating cancerin a subject comprising administering to the subject an effective amountof a strain of Bifidobacterium animalis ssp. lactis comprising a genomehaving at least 95% sequence identity to the genome of Bifidobacteriumanimalis ssp. lactis Strain A (ATCC Deposit Number PTA-125097) to treatthe cancer.
 135. The method of claim 134, wherein the cancer is anon-small cell lung cancer, a colorectal cancer, a triple negativebreast cancer, a bladder cancer, a gastroesophageal cancer, a renal cellcarcinoma, or a solid tumor.
 136. The method of claim 134, wherein thebacterial composition is administered orally.
 137. The method of claim134, wherein the bacterial composition is formulated as a capsule or atablet.
 138. The method of claim 134, wherein the bacterial compositioncomprises at least 7.5×10¹⁰ colony forming units (CFUs) ofBifidobacterium animalis ssp. lactis.
 139. The method of claim 134,wherein the bacterial composition is administered at least once daily.140. The method of claim 134, wherein the bacterial composition isadministered twice daily.
 141. The method of claim 134, wherein thebacterial composition is administered in two or more doses.
 142. Themethod of claim 134, wherein the method further comprises administeringto the subject a second cancer therapy.
 143. The method of claim 142,wherein the second cancer therapy is administered once every 1 week, 2weeks, 3 weeks, 4 weeks, or 5 weeks.
 144. The method of claim 142,wherein the second cancer therapy comprises cancer immunotherapy. 145.The method of claim 144, wherein the cancer immunotherapy comprisesadministering an immune checkpoint inhibitor to the subject.
 146. Themethod of claim 145, wherein the immune checkpoint inhibitor is ananti-PD-1 antibody.
 147. The method of claim 146, wherein the anti-PD-1antibody is nivolumab or pembrolizumab.
 148. The method of claim 147,wherein pembrolizumab is administered intravenously.
 149. The method ofclaim 145, wherein the immune checkpoint inhibitor is an anti-PD-L1antibody.
 150. The method of claim 149, wherein the anti-PD-L1 antibodyis atezolizumab, avelumab, or durvalumab.
 151. The method of claim 149,wherein the anti-PD-L1 antibody is administered intravenously.
 152. Themethod of claim 145, wherein the immune checkpoint inhibitor is ananti-CTLA-4 antibody.
 153. The method of claim 152, wherein theanti-CTLA-4 antibody is ipilimumab.
 154. The method of claim 153,wherein ipilimumab is administered intravenously.
 155. A pharmaceuticalcomposition formulated for oral administration comprising a strain ofBifidobacterium animalis ssp. Lactis comprising a genome having at least95% sequence identity to the genome of Bifidobacterium animalis ssp.lactis Strain A (ATCC Deposit Number PTA-125097) and a pharmaceuticallyacceptable carrier with an enteric coating.
 156. The pharmaceuticalcomposition of claim 155, wherein the pharmaceutical composition isformulated in an enteric coated capsule.
 157. The pharmaceuticalcomposition of claim 155, wherein the enteric coating is a coating forduodenal release at a pH of about 5.5-6.2.
 158. The pharmaceuticalcomposition of claim 155, wherein the pharmaceutical compositioncomprises an enteric coated tablet.
 159. The pharmaceutical compositionof claim 155, wherein the Bifidobacterium animalis ssp. Lactis Strainare live bacteria or freeze-dried.